automation-bio-atomic-force-microscope-measurements-on-hundreds-c

Automation of Bio-Atomic Force Microscope Measurements on Hundreds of <em>C. albicans</em> Cells

The method presented in this paper aims to automate Bio-AFM experiments and the recording of force curves. Using this method, it is possible to record ...

Université de Toulouse, CNRS, Toulouse, France

This work was devoted to the first AFM investigation of the adhesion force to pig gastric mucin (PGM) using Lactococcus lactis as the model for lactic acid bacteria. The PGM coating on polystyrene was characterized using a complementary set of multiscale analytical methods, including AFM (HarmoniX mode), XPS, and the sessile drop method. The PGM layer, which was mainly composed of C-O, C-N, COOH, CONH, and sulfur-related species (protein core and oligosaccharide side chains), was quite homogeneous and hydrophilic, with an estimated thickness of 3.4 nm. L. lactis cells were immobilized on the AFM tip (lacto probe) and used as a force probe to measure the interaction forces between bacteria and PGM-coated polystyrene on the nanoscale. After mucin adsorption, adhesion force levels were lower because of the interplay of electrostatic, hydrophilic, and steric repulsions. For example, the adhesion forces of the lacto probe to bare and PGM-coated polymer were 0.74 +/- 0.10 and 0.12 +/- 0.06 nN, respectively. The shape analysis of retraction force-distance curves highlighted the contribution of both nonspecific and specific forces (ligand/receptor bonding). The lacto probe concept and the associated AFM measurements may now provide a powerful framework for understanding interaction mechanisms between mucins and lactic acid bacteria.

Probing in vitro interactions between Lactococcus lactis and mucins using AFM.

Yeast cells are surrounded by a thick cell wall, the composition and structure of which have been characterized by biochemical and genetic methods. In this study, we used atomic force microscopy (AFM) to visualize the cell surface topography and to determine cell wall nanomechanical properties of yeast mutants defective in cell wall architecture. While all mutants investigated showed some alteration in cell surface topography, this alteration was particularly salient in mutants defective in beta-glucan elongation (gas1), chitin synthesis (chs3) and cross-linkages between chitin and beta-glucan (crh1crh2). In addition, these alterations in surface topology were accompanied by increased roughness of the cell. From force-indentation curves, the Young's modulus was determined, as it gives a measure of the elasticity of the cell wall. A value of approximately 1.6 MPa was obtained for the cell walls of the wild-type strain in exponential and stationary phases of growth. The same value was measured in a mnn9 mutant defective in protein mannosylation, and was two-fold reduced in a mutant with reduced beta-glucan (fks1Delta and knr4Delta), only in the stationary phase of growth. In contrast, the elasticity was dramatically reduced in mutants defective in chitin synthesis (chs3Delta), beta-glucan elongation (gas1Delta) and, even more remarkably, in a crh1Deltacrh2Delta mutant defective in the enzymes that catalyse cross-linkages of chitin to beta-glucan. Taken together, these results provide direct physical evidence that the nanomechanical properties of the yeast cell wall are mainly dependent on cross-links and cell wall remodelling, rather than on cell wall composition or thickness.

An atomic force microscopy analysis of yeast mutants defective in cell wall architecture.

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.

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

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.

Atomic Force Microscopy and pharmacology: from microbiology to cancerology.

Loss of T-tubules (TT), sarcolemmal invaginations of cardiomyocytes (CMs), was recently identified as a general heart failure (HF) hallmark. However, whether TT per se or the overall sarcolemma is altered during HF process is still unknown. In this study, we directly examined sarcolemmal surface topography and physical properties using Atomic Force Microscopy (AFM) in living CMs from healthy and failing mice hearts. We confirmed the presence of highly organized crests and hollows along myofilaments in isolated healthy CMs. Sarcolemma topography was tightly correlated with elasticity, with crests stiffer than hollows and related to the presence of few packed subsarcolemmal mitochondria (SSM) as evidenced by electron microscopy. Three days after myocardial infarction (MI), CMs already exhibit an overall sarcolemma disorganization with general loss of crests topography thus becoming smooth and correlating with a decreased elasticity while interfibrillar mitochondria (IFM), myofilaments alignment and TT network were unaltered. End-stage post-ischemic condition (15days post-MI) exacerbates overall sarcolemma disorganization with, in addition to general loss of crest/hollow periodicity, a significant increase of cell surface stiffness. Strikingly, electron microscopy revealed the total depletion of SSM while some IFM heaps could be visualized beneath the membrane. Accordingly, mitochondrial Ca(2+) studies showed a heterogeneous pattern between SSM and IFM in healthy CMs which disappeared in HF. In vitro, formamide-induced sarcolemmal stress on healthy CMs phenocopied post-ischemic kinetics abnormalities and revealed initial SSM death and crest/hollow disorganization followed by IFM later disarray which moved toward the cell surface and structured heaps correlating with TT loss. This study demonstrates that the loss of crest/hollow organization of CM surface in HF occurs early and precedes disruption of the TT network. It also highlights a general stiffness increased of the CM surface most likely related to atypical IFM heaps while SSM died during HF process. Overall, these results indicate that initial sarcolemmal stress leading to SSM death could underlie subsequent TT disarray and HF setting. 

Atomic force and electron microscopic-based study of sarcolemmal surface of living cardiomyocytes unveils unexpected mitochondrial shift in heart failure.

Candida albicans is an opportunistic pathogen. It adheres to mammalian cells through a variety of adhesins that interact with host ligands. The spatial organization of these adhesins on the cellular interface is however poorly understood, mainly because of the lack of an instrument able to track single molecules on single cells. In this context, the atomic force microscope (AFM) makes it possible to analyze the force signature of single proteins on single cells. The present study is dedicated to the mapping of the adhesive properties of C. albicans cells. We observed that the adhesins at the cell surface were organized in nanodomains composed of free or aggregated mannoproteins. This was demonstrated by the use of functionalized AFM tips and synthetic amyloid forming/disrupting peptides. This direct visualization of amyloids nanodomains will help in understanding the virulence factors of C. albicans.

Multiparametric imaging of adhesive nanodomains at the surface of Candida albicans by atomic force microscopy.

In this study we focused on the mechanism of colistin resistance in Klebsiella pneumoniae.

Unravelling of a mechanism of resistance to colistin in Klebsiella pneumoniae using atomic force microscopy.

Structural and mechanical mapping at the nanoscale by novel high-speed multiparametric Quantitative Imaging (QI) and PeakForce Quantitative Nanomechanical Mapping (PF-QNM) AFM modes was compared to the classical Force Volume (FV) mapping for the case of living Pseudomonas aeruginosa bacterial cells. QI and PF-QNM modes give results consistent with FV for the whole cells in terms of morphology and elastic modulus, while providing higher resolution and shorter acquisition time. As an important complement, the influence of scanning parameters on elastic modulus values was explored for small 0.2(2)μm(2) central area on top of cells. The modulus decreases with the indentation depth due to the effect of the hard cell wall, while it increases vs. tip oscillation frequency, displaying viscoelastic behaviour of the living bacterial cells. The ability of different AFM modes to follow correctly the bacteria viscoelastic behaviour at high oscillation frequency was tested. 

High speed indentation measures by FV, QI and QNM introduce a new understanding of bionanomechanical experiments.

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.

Biophysical properties of cardiomyocyte surface explored by multiparametric AFM.

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.

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

Atomic force microscopy (AFM) is emerging as an innovative tool to phenotype the brain. This study demonstrates the utility of AFM to determine nanomechanical and nanostructural features of the murine dorsolateral frontal cortex from weaning to adulthood. We found an increase in tissue stiffness of the primary somatosensory cortex with age, along with an increased cortical mechanical heterogeneity. To characterize the features potentially responsible for this heterogeneity, we applied AFM scan mode to directly image the topography of thin sections of the primary somatosensory cortical layers II/III, IV and V/VI. Topographical mapping of the cortical layers at successive ages showed progressive smoothing of the surface. Topographical images were also compared with histochemically derived morphological information, which demonstrated the deposition of perineuronal nets, important extracellular components and markers of maturity. Our work demonstrates that high-resolution AFM images can be used to determine the nanostructural properties of cortical maturation, well beyond embryonic and postnatal development. Furthermore, it may offer a new method for brain phenotyping and screening to uncover topographical changes in early stages of neurodegenerative diseases.

Nanoscale structural mapping as a measure of maturation in the murine frontal cortex.

Bacterial adhesion is currently the subject of increased interest from the research community, leading to fast progress in our understanding of this complex phenomenon. Resent research within this field has documented the important roles played by glycans for bacterial surface adhesion, either through interaction with lectins or with other glycans. In parallel with this increased interest for and understanding of bacterial adhesion, there has been a growth in the sophistication and use of sensitive force probes for single-molecule and single cell studies. In this review, we highlight how the sensitive force probes atomic force microscopy (AFM) and optical tweezers (OT) have contributed to clarifying the mechanisms underlying bacterial adhesion to glycosylated surfaces in general and mucosal surfaces in particular. We also describe research areas where these techniques have not yet been applied, but where their capabilities appear appropriate to advance our understanding.

The Role of Glycans in Bacterial Adhesion to Mucosal Surfaces: How Can Single-Molecule Techniques Advance Our Understanding?

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.

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

Lactic acid bacteria, in particular Lactococcus lactis, are widely used in the food industry, for the control and/or the protection of the manufacturing processes of fermented food. While L. lactis has been reported to form compact and uniform biofilms it was recently shown that certain strains able to display pili at their surface form more complex biofilms exhibiting heterogeneous and aerial structures. As the impact of those biofilm structures on the biomechanical properties of the biofilms is poorly understood, these were investigated using AFM force spectroscopy and imaging. Three types of strains were used i.e., a control strain devoid of pili and surface mucus-binding protein, a strain displaying pili but no mucus-binding proteins and a strain displaying both pili and a mucus-binding protein. To identify potential correlations between the nanomechanical measurements and the biofilm architecture, 24-h old biofilms were characterized by confocal laser scanning microscopy. Globally the strains devoid of pili displayed smoother and stiffer biofilms (Young Modulus of 4-100 kPa) than those of piliated strains (Young Modulus around 0.04-0.1 kPa). Additional display of a mucus-binding protein did not affect the biofilm stiffness but made the biofilm smoother and more compact. Finally, we demonstrated the role of pili in the biofilm cohesiveness by monitoring the homotypic adhesion of bacteria to the biofilm surface. These results will help to understand the role of pili and mucus-binding proteins withstanding external forces.

Article	Year
Probing in vitro interactions between Lactococcus lactis and mucins using AFM. Langmuir : the ACS journal of surfaces and colloids\| PubMed ID: 20540551	2010
An atomic force microscopy analysis of yeast mutants defective in cell wall architecture. Yeast (Chichester, England)\| PubMed ID: 20602335	2010
Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments. Nanotechnology\| PubMed ID: 21891839	2011
Atomic Force Microscopy and pharmacology: from microbiology to cancerology. Biochimica et biophysica acta\| PubMed ID: 24291690	2014
Atomic force and electron microscopic-based study of sarcolemmal surface of living cardiomyocytes unveils unexpected mitochondrial shift in heart failure. Journal of molecular and cellular cardiology\| PubMed ID: 24839910	2014
Multiparametric imaging of adhesive nanodomains at the surface of Candida albicans by atomic force microscopy. Nanomedicine : nanotechnology, biology, and medicine\| PubMed ID: 25101882	2015
Unravelling of a mechanism of resistance to colistin in Klebsiella pneumoniae using atomic force microscopy. The Journal of antimicrobial chemotherapy\| PubMed ID: 26017037	2015
High speed indentation measures by FV, QI and QNM introduce a new understanding of bionanomechanical experiments. Micron (Oxford, England : 1993)\| PubMed ID: 27023832	2016
Biophysical properties of cardiomyocyte surface explored by multiparametric AFM. Journal of structural biology\| PubMed ID: 28263874	2017
Cell biology of microbes and pharmacology of antimicrobial drugs explored by Atomic Force Microscopy. Seminars in cell & developmental biology\| PubMed ID: 28668355	2018
Nanoscale structural mapping as a measure of maturation in the murine frontal cortex. Brain structure & function\| PubMed ID: 28779306	2018
The Role of Glycans in Bacterial Adhesion to Mucosal Surfaces: How Can Single-Molecule Techniques Advance Our Understanding? Microorganisms\| PubMed ID: 29734645	2018
Changes in nanomechanical properties and adhesion dynamics of algal cells during their growth. Bioelectrochemistry (Amsterdam, Netherlands)\| PubMed ID: 30826730	2019
Pili and other surface proteins influence the structure and the nanomechanical properties of Lactococcus lactis biofilms. Scientific reports\| PubMed ID: 33649417	2021

Etienne Dague

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