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Obořilová R, Šimečková H, Pastucha M, Klimovič Š, Víšová I, Přibyl J, Vaisocherová-Lísalová H, Pantůček R, Skládal P, Mašlaňová I, Farka Z. Atomic force microscopy and surface plasmon resonance for real-time single-cell monitoring of bacteriophage-mediated lysis of bacteria. NANOSCALE 2021; 13:13538-13549. [PMID: 34477758 DOI: 10.1039/d1nr02921e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The growing incidence of multidrug-resistant bacterial strains presents a major challenge in modern medicine. Antibiotic resistance is often exhibited by Staphylococcus aureus, which causes severe infections in human and animal hosts and leads to significant economic losses. Antimicrobial agents with enzymatic activity (enzybiotics) and phage therapy represent promising and effective alternatives to classic antibiotics. However, new tools are needed to study phage-bacteria interactions and bacterial lysis with high resolution and in real-time. Here, we introduce a method for studying the lysis of S. aureus at the single-cell level in real-time using atomic force microscopy (AFM) in liquid. We demonstrate the ability of the method to monitor the effect of the enzyme lysostaphin on S. aureus and the lytic action of the Podoviridae phage P68. AFM allowed the topographic and biomechanical properties of individual bacterial cells to be monitored at high resolution over the course of their lysis, under near-physiological conditions. Changes in the stiffness of S. aureus cells during lysis were studied by analyzing force-distance curves to determine Young's modulus. This allowed observing a progressive decline in cellular stiffness corresponding to the disintegration of the cell envelope. The AFM experiments were complemented by surface plasmon resonance (SPR) experiments that provided information on the kinetics of phage-bacterium binding and the subsequent lytic processes. This approach forms the foundation of an innovative framework for studying the lysis of individual bacteria that may facilitate the further development of phage therapy.
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Affiliation(s)
- Radka Obořilová
- Department of Biochemistry, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
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2
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Kiss B, Bozó T, Mudra D, Tordai H, Herényi L, Kellermayer M. Development, structure and mechanics of a synthetic E. coli outer membrane model. NANOSCALE ADVANCES 2021; 3:755-766. [PMID: 36133844 PMCID: PMC9418885 DOI: 10.1039/d0na00977f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/09/2020] [Indexed: 06/16/2023]
Abstract
The outer membrane (OM) of Gram-negative bacteria is a complex asymmetric bilayer containing lipids, lipopolysaccharides (LPS) and proteins. While it is a mechanical and chemical barrier, it is also the primary surface of bacterial recognition processes that involve infection by and of the bacterium. Uncovering the mechanisms of these biological functions has been hampered by the lack of suitable model systems. Here we report the step-by-step assembly of a synthetic OM model from its fundamental components. To enable the efficient formation of a supported lipid bilayer at room temperature, dimyristoyl-phosphocholine (DMPC) was used as the lipid component to which we progressively added LPS and OM proteins. The assembled system enabled us to explore the contribution of the molecular components to the topographical structure and stability of the OM. We found that LPS prefers solid-state membrane regions and forms stable vesicles in the presence of divalent cations. LPS can gradually separate from DMPC membranes to form independent vesicles, pointing at the dynamic nature of the lipid-LPS system. The addition of OM proteins from E. coli and saturating levels of LPS to DMPC liposomes resulted in a thicker and more stable bilayer the surface of which displayed a nanoscale texture formed of parallel, curved, long (>500 nm) stripes spaced apart with a 15 nm periodicity. The synthetic membrane may facilitate the investigation of binding and recognition processes on the surface of Gram-negative bacteria.
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Affiliation(s)
- Bálint Kiss
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
| | - Tamás Bozó
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
| | - Dorottya Mudra
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
| | - Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
| | - Levente Herényi
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
| | - Miklós Kellermayer
- Department of Biophysics and Radiation Biology, Semmelweis University Budapest Hungary
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3
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Saffioti NA, Cavalcanti-Adam EA, Pallarola D. Biosensors for Studies on Adhesion-Mediated Cellular Responses to Their Microenvironment. Front Bioeng Biotechnol 2020; 8:597950. [PMID: 33262979 PMCID: PMC7685988 DOI: 10.3389/fbioe.2020.597950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/12/2020] [Indexed: 12/28/2022] Open
Abstract
Cells interact with their microenvironment by constantly sensing mechanical and chemical cues converting them into biochemical signals. These processes allow cells to respond and adapt to changes in their environment, and are crucial for most cellular functions. Understanding the mechanism underlying this complex interplay at the cell-matrix interface is of fundamental value to decipher key biochemical and mechanical factors regulating cell fate. The combination of material science and surface chemistry aided in the creation of controllable environments to study cell mechanosensing and mechanotransduction. Biologically inspired materials tailored with specific bioactive molecules, desired physical properties and tunable topography have emerged as suitable tools to study cell behavior. Among these materials, synthetic cell interfaces with built-in sensing capabilities are highly advantageous to measure biophysical and biochemical interaction between cells and their environment. In this review, we discuss the design of micro and nanostructured biomaterials engineered not only to mimic the structure, properties, and function of the cellular microenvironment, but also to obtain quantitative information on how cells sense and probe specific adhesive cues from the extracellular domain. This type of responsive biointerfaces provides a readout of mechanics, biochemistry, and electrical activity in real time allowing observation of cellular processes with molecular specificity. Specifically designed sensors based on advanced optical and electrochemical readout are discussed. We further provide an insight into the emerging role of multifunctional micro and nanosensors to control and monitor cell functions by means of material design.
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Affiliation(s)
- Nicolás Andrés Saffioti
- Instituto de Nanosistemas, Universidad Nacional de General San Martín, San Martín, Argentina
| | | | - Diego Pallarola
- Instituto de Nanosistemas, Universidad Nacional de General San Martín, San Martín, Argentina
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4
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Sandin JN, Aryal SP, Wilkop T, Richards CI, Grady ME. Near Simultaneous Laser Scanning Confocal and Atomic Force Microscopy (Conpokal) on Live Cells. J Vis Exp 2020:10.3791/61433. [PMID: 32865532 PMCID: PMC7680637 DOI: 10.3791/61433] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
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.
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Affiliation(s)
- Joree N Sandin
- Department of Mechanical Engineering, University of Kentucky
| | | | - Thomas Wilkop
- Department of Physiology, University of Kentucky; UK Light Microscopy Core, University of Kentucky
| | - Christopher I Richards
- Department of Chemistry, University of Kentucky; UK Light Microscopy Core, University of Kentucky
| | - Martha E Grady
- Department of Mechanical Engineering, University of Kentucky;
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5
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Pasquina-Lemonche L, Burns J, Turner RD, Kumar S, Tank R, Mullin N, Wilson JS, Chakrabarti B, Bullough PA, Foster SJ, Hobbs JK. The architecture of the Gram-positive bacterial cell wall. Nature 2020; 582:294-297. [PMID: 32523118 PMCID: PMC7308169 DOI: 10.1038/s41586-020-2236-6] [Citation(s) in RCA: 181] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2020] [Indexed: 02/05/2023]
Abstract
The primary structural component of the bacterial cell wall is peptidoglycan, which is essential for viability and the synthesis of which is the target for crucial antibiotics1,2. Peptidoglycan is a single macromolecule made of glycan chains crosslinked by peptide side branches that surrounds the cell, acting as a constraint to internal turgor1,3. In Gram-positive bacteria, peptidoglycan is tens of nanometres thick, generally portrayed as a homogeneous structure that provides mechanical strength4-6. Here we applied atomic force microscopy7-12 to interrogate the morphologically distinct Staphylococcus aureus and Bacillus subtilis species, using live cells and purified peptidoglycan. The mature surface of live cells is characterized by a landscape of large (up to 60 nm in diameter), deep (up to 23 nm) pores constituting a disordered gel of peptidoglycan. The inner peptidoglycan surface, consisting of more nascent material, is much denser, with glycan strand spacing typically less than 7 nm. The inner surface architecture is location dependent; the cylinder of B. subtilis has dense circumferential orientation, while in S. aureus and division septa for both species, peptidoglycan is dense but randomly oriented. Revealing the molecular architecture of the cell envelope frames our understanding of its mechanical properties and role as the environmental interface13,14, providing information complementary to traditional structural biology approaches.
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Affiliation(s)
- L Pasquina-Lemonche
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
- The Florey Institute, University of Sheffield, Sheffield, UK
| | - J Burns
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - R D Turner
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | - S Kumar
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - R Tank
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - N Mullin
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - J S Wilson
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - B Chakrabarti
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK
| | - P A Bullough
- Krebs Institute, University of Sheffield, Sheffield, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - S J Foster
- Krebs Institute, University of Sheffield, Sheffield, UK.
- The Florey Institute, University of Sheffield, Sheffield, UK.
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.
| | - J K Hobbs
- Krebs Institute, University of Sheffield, Sheffield, UK.
- Department of Physics and Astronomy, University of Sheffield, Sheffield, UK.
- The Florey Institute, University of Sheffield, Sheffield, UK.
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6
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Probing the surface ultrastructure of Brevibacillus laterosporus using atomic force microscopy. Micron 2020; 131:102827. [PMID: 31951938 DOI: 10.1016/j.micron.2020.102827] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/12/2020] [Accepted: 01/12/2020] [Indexed: 11/21/2022]
Abstract
One of the main obstacles to studying the surface ultrastructure of microbial cells by atomic force microscopy (AFM) is determining how to immobilize live cells on the AFM substrates. Each method has its own advantages and disadvantages. The aim of this study was to characterize a new simple and inexpensive method using two types of polyethersulfone (PES) membrane filters that differ in pore size (micropore and nanopore) to immobilize live and dead Brevibacillus laterosporus for AFM imaging. B. laterosporus was easily trapped by the microporous PES membrane, facilitating the successful AFM scanning of the bacterial surface ultrastructure. In addition, B. laterosporus strongly attached to the nanoporous membranes and withstood the pulling forces exerted by the AFM tip during scanning. These methods of immobilization did not affect the cell viability. The nanostructure and roughness of the bacterial surface were also observed for live, fixed, and air-dried cells. Live and dead bacteria displayed similar morphologies at low resolution, while at high resolution, live bacteria displayed a more convoluted surface ("brain-like structure").
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7
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Benn G, Pyne ALB, Ryadnov MG, Hoogenboom BW. Imaging live bacteria at the nanoscale: comparison of immobilisation strategies. Analyst 2019; 144:6944-6952. [PMID: 31620716 PMCID: PMC7138128 DOI: 10.1039/c9an01185d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/10/2019] [Indexed: 12/17/2022]
Abstract
Atomic force microscopy (AFM) provides an effective, label-free technique enabling the imaging of live bacteria under physiological conditions with nanometre precision. However, AFM is a surface scanning technique, and the accuracy of its performance requires the effective and reliable immobilisation of bacterial cells onto substrates. Here, we compare the effectiveness of various chemical approaches to facilitate the immobilisation of Escherichia coli onto glass cover slips in terms of bacterial adsorption, viability and compatibility with correlative imaging by fluorescence microscopy. We assess surface functionalisation using gelatin, poly-l-lysine, Cell-Tak™, and Vectabond®. We describe how bacterial immobilisation, viability and suitability for AFM experiments depend on bacterial strain, buffer conditions and surface functionalisation. We demonstrate the use of such immobilisation by AFM images that resolve the porin lattice on the bacterial surface; local degradation of the bacterial cell envelope by an antimicrobial peptide (Cecropin B); and the formation of membrane attack complexes on the bacterial membrane.
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Affiliation(s)
- Georgina Benn
- London Centre for Nanotechnology
, University College London
,
London WC1H 0AH
, UK
.
- Institute of Structural and Molecular Biology
, University College London
,
London WC1E 6BT
, UK
- National Physical Laboratory
,
Hampton Road
, Teddington TW11 0LW
, UK
| | - Alice L. B. Pyne
- London Centre for Nanotechnology
, University College London
,
London WC1H 0AH
, UK
.
- Department of Materials Science and Engineering
, University of Sheffield
,
S1 3JD
, UK
| | - Maxim G. Ryadnov
- National Physical Laboratory
,
Hampton Road
, Teddington TW11 0LW
, UK
- Department of Physics
, King's College London
,
Strand Lane
, London WC2R 2LS
, UK
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology
, University College London
,
London WC1H 0AH
, UK
.
- Institute of Structural and Molecular Biology
, University College London
,
London WC1E 6BT
, UK
- Department of Physics & Astronomy
, University College London
,
London WC1E 6BT
, UK
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8
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Nguyen DHK, Loebbe C, Linklater DP, Xu X, Vrancken N, Katkus T, Juodkazis S, Maclaughlin S, Baulin V, Crawford RJ, Ivanova EP. The idiosyncratic self-cleaning cycle of bacteria on regularly arrayed mechano-bactericidal nanostructures. NANOSCALE 2019; 11:16455-16462. [PMID: 31451827 DOI: 10.1039/c9nr05923g] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Nanostructured mechano-bactericidal surfaces represent a promising technology to prevent the incidence of microbial contamination on a variety of surfaces and to avoid bacterial infection, particularly with antibiotic resistant strains. In this work, a regular array of silicon nanopillars of 380 nm height and 35 nm diameter was used to study the release of bacterial cell debris off the surface, following inactivation of the cell due to nanostructure-induced rupture. It was confirmed that substantial bactericidal activity was achieved against Gram-negative Pseudomonas aeruginosa (85% non-viable cells) and only modest antibacterial activity towards Staphylococcus aureus (8% non-viable cells), as estimated by measuring the proportions of viable and non-viable cells via fluorescence imaging. In situ time-lapse AFM scans of the bacteria-nanopillar interface confirmed the removal rate of the dead P. aeruginosa cells from the surface to be approximately 19 minutes per cell, and approximately 11 minutes per cell for dead S. aureus cells. These results highlight that the killing and dead cell detachment cycle for bacteria on these substrata are dependant on the bacterial species and the surface architecture studied and will vary when these two parameters are altered. The outcomes of this work will enhance the current understanding of antibacterial nanostructures, and impact upon the development and implementation of next-generation implants and medical devices.
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Affiliation(s)
- Duy H K Nguyen
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia.
| | | | - Denver P Linklater
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia. and Centre for Microphotonics, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - XiuMei Xu
- IMEC, Kapeldreef 75, Leuven 3001, Belgium
| | - Nandi Vrancken
- IMEC, Kapeldreef 75, Leuven 3001, Belgium and Research Group Electrochemical and Surface Engineering (SURF), Dept. of Materials & Chemistry (MACH), Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Elsene, Belgium
| | - Tomas Katkus
- Centre for Microphotonics, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | - Saulius Juodkazis
- Centre for Microphotonics, Swinburne University of Technology, Hawthorn, VIC 3122, Australia
| | | | - Vladimir Baulin
- Departament d'Enginyeria Química, Universitat Rovira i Virgili Tarragona, Spain
| | - Russell J Crawford
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia.
| | - Elena P Ivanova
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia.
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9
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Alam F, Kumar S, Varadarajan KM. Quantification of Adhesion Force of Bacteria on the Surface of Biomaterials: Techniques and Assays. ACS Biomater Sci Eng 2019; 5:2093-2110. [DOI: 10.1021/acsbiomaterials.9b00213] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fahad Alam
- Biomaterials Processing and Characterization Laboratory, Materials Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- Department of Mechanical and Materials Engineering, Khalifa University of Science and Technology, Masdar Institute, Masdar City, Abu Dhabi United Arab Emirates
| | - Shanmugam Kumar
- Department of Mechanical and Materials Engineering, Khalifa University of Science and Technology, Masdar Institute, Masdar City, Abu Dhabi United Arab Emirates
| | - Kartik M. Varadarajan
- Department of Orthopaedic Surgery, Harvard Medical School, A-111, 25 Shattuck Street, Boston, Massachusetts 02115, United States
- Department of Orthopaedic Surgery, Harris Orthopaedics Laboratory, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, United States
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10
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Elbourne A, Chapman J, Gelmi A, Cozzolino D, Crawford RJ, Truong VK. Bacterial-nanostructure interactions: The role of cell elasticity and adhesion forces. J Colloid Interface Sci 2019; 546:192-210. [PMID: 30921674 DOI: 10.1016/j.jcis.2019.03.050] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 02/07/2023]
Abstract
The attachment of single-celled organisms, namely bacteria and fungi, to abiotic surfaces is of great interest to both the scientific and medical communities. This is because the interaction of such cells has important implications in a range of areas, including biofilm formation, biofouling, antimicrobial surface technologies, and bio-nanotechnologies, as well as infection development, control, and mitigation. While central to many biological phenomena, the factors which govern microbial surface attachment are still not fully understood. This lack of understanding is a direct consequence of the complex nature of cell-surface interactions, which can involve both specific and non-specific interactions. For applications involving micro- and nano-structured surfaces, developing an understanding of such phenomenon is further complicated by the diverse nature of surface architectures, surface chemistry, variation in cellular physiology, and the intended technological output. These factors are extremely important to understand in the emerging field of antibacterial nanostructured surfaces. The aim of this perspective is to re-frame the discussion surrounding the mechanism of nanostructured-microbial surface interactions. Broadly, the article reviews our current understanding of these phenomena, while highlighting the knowledge gaps surrounding the adhesive forces which govern bacterial-nanostructure interactions and the role of cell membrane rigidity in modulating surface activity. The roles of surface charge, cell rigidity, and cell-surface adhesion force in bacterial-surface adsorption are discussed in detail. Presently, most studies have overlooked these areas, which has left many questions unanswered. Further, this perspective article highlights the numerous experimental issues and misinterpretations which surround current studies of antibacterial nanostructured surfaces.
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Affiliation(s)
- Aaron Elbourne
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia; Nanobiotechnology Laboratory, RMIT University, Melbourne, VIC 3001, Australia.
| | - James Chapman
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia; Nanobiotechnology Laboratory, RMIT University, Melbourne, VIC 3001, Australia
| | - Amy Gelmi
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia
| | - Daniel Cozzolino
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia
| | - Russell J Crawford
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia; Nanobiotechnology Laboratory, RMIT University, Melbourne, VIC 3001, Australia
| | - Vi Khanh Truong
- School of Science, College of Science, Engineering and Health, RMIT University, Melbourne, VIC 3001, Australia; Nanobiotechnology Laboratory, RMIT University, Melbourne, VIC 3001, Australia
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11
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Cheptsov VS, Tsypina SI, Minaev NV, Yusupov VI, Chichkov BN. New microorganism isolation techniques with emphasis on laser printing. Int J Bioprint 2018; 5:165. [PMID: 32596530 PMCID: PMC7294688 DOI: 10.18063/ijb.v5i1.165] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 10/16/2018] [Indexed: 01/05/2023] Open
Abstract
The study of biodiversity, growth, development, and metabolism of cultivated microorganisms is an integral part of modern microbiological, biotechnological, and medical research. Such studies require the development of new methods of isolation, cultivation, manipulation, and study of individual bacterial cells and their consortia. To this end, in recent years, there has been an active development of different isolation and three-dimensional cell positioning methods. In this review, the optical tweezers, surface heterogeneous functionalization, multiphoton lithography, microfluidic techniques, and laser printing are reviewed. Laser printing is considered as one of the most promising techniques and is discussed in detail.
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Affiliation(s)
- V S Cheptsov
- Department of Soil Science, Lomonosov Moscow State University, 11999 Moscow, Russia
| | - S I Tsypina
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - N V Minaev
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - V I Yusupov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia
| | - B N Chichkov
- Research Center "Crystallography and Photonics" RAS, Institute of Photonic Technologies, Troitsk, Moscow, Russia.,Institut für Quantenoptik, Leibniz Universität Hannover, Welfengarten, 30167, Hannover
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12
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Nievergelt AP, Brillard C, Eskandarian HA, McKinney JD, Fantner GE. Photothermal Off-Resonance Tapping for Rapid and Gentle Atomic Force Imaging of Live Cells. Int J Mol Sci 2018; 19:E2984. [PMID: 30274330 PMCID: PMC6213139 DOI: 10.3390/ijms19102984] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 01/20/2023] Open
Abstract
Imaging living cells by atomic force microscopy (AFM) promises not only high-resolution topographical data, but additionally, mechanical contrast, both of which are not obtainable with other microscopy techniques. Such imaging is however challenging, as cells need to be measured with low interaction forces to prevent either deformation or detachment from the surface. Off-resonance modes which periodically probe the surface have been shown to be advantageous, as they provide excellent force control combined with large amplitudes, which help reduce lateral force interactions. However, the low actuation frequency in traditional off-resonance techniques limits the imaging speed significantly. Using photothermal actuation, we probe the surface by directly actuating the cantilever. Due to the much smaller mass that needs to be actuated, the achievable measurement frequency is increased by two orders of magnitude. Additionally, photothermal off-resonance tapping (PORT) retains the precise force control of conventional off-resonance modes and is therefore well suited to gentle imaging. Here, we show how photothermal off-resonance tapping can be used to study live cells by AFM. As an example of imaging mammalian cells, the initial attachment, as well as long-term detachment, of human thrombocytes is presented. The membrane disrupting effect of the antimicrobial peptide CM-15 is shown on the cell wall of Escherichia coli. Finally, the dissolution of the cell wall of Bacillus subtilis by lysozyme is shown. Taken together, these evolutionarily disparate forms of life exemplify the usefulness of PORT for live cell imaging in a multitude of biological disciplines.
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Affiliation(s)
- Adrian P Nievergelt
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Charlène Brillard
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Haig A Eskandarian
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
- UPKIN, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - John D McKinney
- UPKIN, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Georg E Fantner
- Laboratory for Bio- and Nano-Instrumentation, Swiss Federal Institute of Technology Lausanne (EPFL), 1015 Lausanne, Switzerland.
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13
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Martinez-Rivas A, González-Quijano GK, Proa-Coronado S, Séverac C, Dague E. Methods of Micropatterning and Manipulation of Cells for Biomedical Applications. MICROMACHINES 2017; 8:E347. [PMID: 30400538 PMCID: PMC6187909 DOI: 10.3390/mi8120347] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 12/12/2022]
Abstract
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.
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Affiliation(s)
- Adrian Martinez-Rivas
- CIC, Instituto Politécnico Nacional (IPN), Av. Juan de Dios Bátiz S/N, Nueva Industrial Vallejo, 07738 Mexico City, Mexico.
| | - Génesis K González-Quijano
- CONACYT-CNMN, Instituto Politécnico Nacional (IPN), Av. Luis Enrique Erro s/n, Nueva Industrial Vallejo, 07738 Mexico City, Mexico.
| | - Sergio Proa-Coronado
- ENCB, Instituto Politécnico Nacional (IPN), Av. Wilfrido Massieu, Unidad Adolfo López Mateos, 07738 Mexico City, Mexico.
| | | | - Etienne Dague
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France.
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Zorila FL, Ionescu C, Craciun LS, Zorila B. Atomic force microscopy study of morphological modifications induced by different decontamination treatments on Escherichia coli. Ultramicroscopy 2017; 182:226-232. [PMID: 28728044 DOI: 10.1016/j.ultramic.2017.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 04/30/2017] [Indexed: 10/19/2022]
Abstract
In this paper we used atomic force microscopy (AFM) to investigate the surface morphology of Escherichia coli, after being subjected to decontamination treatments, at sub-MICs levels (minimal inhibitory concentrations), with different disinfectants used in hospitals, pharmaceutical, food industry and even in our home, as an essential means to prevent the spreading of microorganisms. This article focuses on different morphological modifications adopted by E. coli cells as responses to the different modes of action of these substances. For high-resolution AFM images bacterial cells were immobilized on mica (Muscovite) disks. Each kind of treatment induces its distinct morphological changes, due to different mechanisms of action.
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Affiliation(s)
- Florina Lucica Zorila
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului St., POB MG-6, 077125 Bucharest, Magurele, Romania; Department of Genetics, Faculty of Biology, University of Bucharest, Bucharest, Romania.
| | - Cristina Ionescu
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului St., POB MG-6, 077125 Bucharest, Magurele, Romania
| | - Liviu Stefan Craciun
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului St., POB MG-6, 077125 Bucharest, Magurele, Romania
| | - Bogdan Zorila
- "Horia Hulubei" National Institute for Physics and Nuclear Engineering, 30 Reactorului St., POB MG-6, 077125 Bucharest, Magurele, Romania; Department of Electricity, Solid Physics and Biophysics, Faculty of Physics, University of Bucharest, Magurele, Romania
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15
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James SA, Hilal N, Wright CJ. Atomic force microscopy studies of bioprocess engineering surfaces - imaging, interactions and mechanical properties mediating bacterial adhesion. Biotechnol J 2017; 12. [PMID: 28488793 DOI: 10.1002/biot.201600698] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/24/2017] [Accepted: 04/10/2017] [Indexed: 12/19/2022]
Abstract
The detrimental effect of bacterial biofilms on process engineering surfaces is well documented. Thus, interest in the early stages of bacterial biofilm formation; in particular bacterial adhesion and the production of anti-fouling coatings has grown exponentially as a field. During this time, Atomic force microscopy (AFM) has emerged as a critical tool for the evaluation of bacterial adhesion. Due to its versatility AFM offers not only insight into the topographical landscape and mechanical properties of the engineering surfaces, but elucidates, through direct quantification the topographical and biomechnical properties of the foulants The aim of this review is to collate the current research on bacterial adhesion, both theoretical and practical, and outline how AFM as a technique is uniquely equipped to provide further insight into the nanoscale world at the bioprocess engineering surface.
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Affiliation(s)
- Sean A James
- Biomaterials, Biofouling and Biofilms Engineering Laboratory (B3EL, System and Process Engineering Center, College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
| | - Nidal Hilal
- Centre for Water Advanced Technologies and Environmental Research (CWATER), College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
| | - Chris J Wright
- Biomaterials, Biofouling and Biofilms Engineering Laboratory (B3EL, System and Process Engineering Center, College of Engineering, Swansea University, Fabian Way, Swansea, SA1 8EN, UK
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16
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Tan SY, Acquah C, Sidhu A, Ongkudon CM, Yon LS, Danquah MK. SELEX Modifications and Bioanalytical Techniques for Aptamer-Target Binding Characterization. Crit Rev Anal Chem 2016; 46:521-37. [PMID: 26980177 DOI: 10.1080/10408347.2016.1157014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The quest to improve the detection of biomolecules and cells in health and life sciences has led to the discovery and characterization of various affinity bioprobes. Libraries of synthetic oligonucleotides (ssDNA/ssRNA) with randomized sequences are employed during Systematic Evolution of Ligands by Exponential Enrichment (SELEX) to select highly specific affinity probes called aptamers. With much focus on the generation of aptamers for a variety of target molecules, conventional SELEX protocols have been modified to develop new and improved SELEX protocols yielding highly specific and stable aptamers. Various techniques have been used to analyze the binding interactions between aptamers and their cognate molecules with associated merits and limitations. This article comprehensively reviews research advancements in the generation of aptamers, analyses physicochemical conditions affecting their binding characteristics to cellular and biomolecular targets, and discusses various field applications of aptameric binding. Biophysical techniques employed in the characterization of the molecular and binding features of aptamers to their cognate targets are also discussed.
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Affiliation(s)
- Sze Y Tan
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Caleb Acquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
| | - Amandeep Sidhu
- b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia.,c Faculty of Health Sciences , Curtin University , Perth , Australia
| | - Clarence M Ongkudon
- d Biotechnology Research Institute , University Malaysia Sabah , Kota Kinabalu , Sabah , Malaysia
| | - L S Yon
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia
| | - Michael K Danquah
- a Department of Chemical Engineering , Curtin University , Sarawak , Malaysia.,b Curtin Sarawak Research Institute , Curtin University , Sarawak , Malaysia
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Shen S, Syal K, Tao N, Wang S. Note: An automated image analysis method for high-throughput classification of surface-bound bacterial cell motions. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:126104. [PMID: 26724085 DOI: 10.1063/1.4937479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a Single-Cell Motion Characterization System (SiCMoCS) to automatically extract bacterial cell morphological features from microscope images and use those features to automatically classify cell motion for rod shaped motile bacterial cells. In some imaging based studies, bacteria cells need to be attached to the surface for time-lapse observation of cellular processes such as cell membrane-protein interactions and membrane elasticity. These studies often generate large volumes of images. Extracting accurate bacterial cell morphology features from these images is critical for quantitative assessment. Using SiCMoCS, we demonstrated simultaneous and automated motion tracking and classification of hundreds of individual cells in an image sequence of several hundred frames. This is a significant improvement from traditional manual and semi-automated approaches to segmenting bacterial cells based on empirical thresholds, and a first attempt to automatically classify bacterial motion types for motile rod shaped bacterial cells, which enables rapid and quantitative analysis of various types of bacterial motion.
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Affiliation(s)
- Simon Shen
- Center for Bioelectronics and Biosensors, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Karan Syal
- Center for Bioelectronics and Biosensors, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Nongjian Tao
- Center for Bioelectronics and Biosensors, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
| | - Shaopeng Wang
- Center for Bioelectronics and Biosensors, The Biodesign Institute at Arizona State University, Tempe, Arizona 85287, USA
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18
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Kilpatrick JI, Revenko I, Rodriguez BJ. Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy. Adv Healthc Mater 2015. [PMID: 26200464 DOI: 10.1002/adhm.201500229] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications.
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Affiliation(s)
- Jason I. Kilpatrick
- Conway Institute of Biomolecular and Biomedical Research; University College Dublin; Belfield Dublin 4 Ireland
| | - Irène Revenko
- Asylum Research an Oxford Instruments Company; 6310 Hollister Avenue Santa Barbara CA 93117 USA
| | - Brian J. Rodriguez
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin; Belfield, Dublin 4, Ireland; School of Physics; University College Dublin; Belfield Dublin 4 Ireland
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Abstract
UNLABELLED Most bacterial cells are enclosed in a single macromolecule of the cell wall polymer, peptidoglycan, which is required for shape determination and maintenance of viability, while peptidoglycan biosynthesis is an important antibiotic target. It is hypothesized that cellular enlargement requires regional expansion of the cell wall through coordinated insertion and hydrolysis of peptidoglycan. Here, a group of (apparent glucosaminidase) peptidoglycan hydrolases are identified that are together required for cell enlargement and correct cellular morphology of Staphylococcus aureus, demonstrating the overall importance of this enzyme activity. These are Atl, SagA, ScaH, and SagB. The major advance here is the explanation of the observed morphological defects in terms of the mechanical and biochemical properties of peptidoglycan. It was shown that cells lacking groups of these hydrolases have increased surface stiffness and, in the absence of SagB, substantially increased glycan chain length. This indicates that, beyond their established roles (for example in cell separation), some hydrolases enable cellular enlargement by making peptidoglycan easier to stretch, providing the first direct evidence demonstrating that cellular enlargement occurs via modulation of the mechanical properties of peptidoglycan. IMPORTANCE Understanding bacterial growth and division is a fundamental problem, and knowledge in this area underlies the treatment of many infectious diseases. Almost all bacteria are surrounded by a macromolecule of peptidoglycan that encloses the cell and maintains shape, and bacterial cells must increase the size of this molecule in order to enlarge themselves. This requires not only the insertion of new peptidoglycan monomers, a process targeted by antibiotics, including penicillin, but also breakage of existing bonds, a potentially hazardous activity for the cell. Using Staphylococcus aureus, we have identified a set of enzymes that are critical for cellular enlargement. We show that these enzymes are required for normal growth and define the mechanism through which cellular enlargement is accomplished, i.e., by breaking bonds in the peptidoglycan, which reduces the stiffness of the cell wall, enabling it to stretch and expand, a process that is likely to be fundamental to many bacteria.
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Palacios-Cuesta M, Cortajarena AL, García O, Rodríguez-Hernández J. Patterning of individual Staphylococcus aureus bacteria onto photogenerated polymeric surface structures. Polym Chem 2015. [DOI: 10.1039/c4py01629g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This manuscript describes the fabrication of bacterial surface arrays by using photolithographic techniques having in addition some particularly interesting features.
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Affiliation(s)
- Marta Palacios-Cuesta
- Department of Chemistry and Properties of Polymers
- Instituto de Ciencia y Tecnología de Polímeros
- (ICTP-CSIC)
- 28006-Madrid
- Spain
| | - Aitziber L. Cortajarena
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit “Unidad de Nanobiotecnología”
- 28049 Madrid
- Spain
| | - Olga García
- Department of Chemistry and Properties of Polymers
- Instituto de Ciencia y Tecnología de Polímeros
- (ICTP-CSIC)
- 28006-Madrid
- Spain
| | - Juan Rodríguez-Hernández
- Department of Chemistry and Properties of Polymers
- Instituto de Ciencia y Tecnología de Polímeros
- (ICTP-CSIC)
- 28006-Madrid
- Spain
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21
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22
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Jauvert E, Palleau E, Dague E, Ressier L. Directed assembly of living Pseudomonas aeruginosa bacteria on PEI patterns generated by nanoxerography for statistical AFM bioexperiments. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21230-21236. [PMID: 25434422 DOI: 10.1021/am506241n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Immobilization of living micro-organisms on predefined areas of substrates is a prerequisite for their characterizations by atomic force microscopy (AFM) in culture media. It remains challenging since micro-organisms should not be denatured but attached strongly enough to be scanned with an AFM tip, in a liquid phase. In this work, a novel approach is proposed to electrostatically assemble biological objects of interest on 2 nm thick polyethylenimine (PEI) patterns fabricated by nanoxerography. This nanoxerography process involves electrostatic trapping of PEI chains on negatively charged patterns written on electret thin films by AFM or electrical microcontact printing. The capability of this approach is demonstrated using a common biological system, Pseudomonas aeruginosa bacteria. These negatively charged bacteria are selectively assembled on large scale arrays of PEI patterns. In contrast to other PEI continuous films commonly used for cell anchoring, these ultrathin PEI patterns strongly attached on the surface do not cause any denaturation of the assembled Pseudomonas aeruginosa bacteria. AFM characterizations of large populations of individual living bacteria in culture media can thus be easily performed through this approach, providing the opportunity to perform representative statistical data analysis. Interestingly, this process may be extended to any negatively charged micro-organism in solution.
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Affiliation(s)
- Eric Jauvert
- Université de Toulouse , LPCNO, INSA-CNRS-UPS, 135 avenue de Rangueil, F-31400 Toulouse, France
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23
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The interplay between cell wall mechanical properties and the cell cycle in Staphylococcus aureus. Biophys J 2014; 107:2538-45. [PMID: 25468333 DOI: 10.1016/j.bpj.2014.10.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/26/2014] [Accepted: 10/08/2014] [Indexed: 11/21/2022] Open
Abstract
The nanoscale mechanical properties of live Staphylococcus aureus cells during different phases of growth were studied by atomic force microscopy. Indentation to different depths provided access to both local cell wall mechanical properties and whole-cell properties, including a component related to cell turgor pressure. Local cell wall properties were found to change in a characteristic manner throughout the division cycle. Splitting of the cell into two daughter cells followed a local softening of the cell wall along the division circumference, with the cell wall on either side of the division circumference becoming stiffer. Once exposed, the newly formed septum was found to be stiffer than the surrounding, older cell wall. Deeper indentations, which were affected by cell turgor pressure, did not show a change in stiffness throughout the division cycle, implying that enzymatic cell wall remodeling and local variations in wall properties are responsible for the evolution of cell shape through division.
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Abstract
Nanobiomechanics of living cells is very important to understand cell-materials interactions. This would potentially help to optimize the surface design of the implanted materials and scaffold materials for tissue engineering. The nanoindentation techniques enable quantifying nanobiomechanics of living cells, with flexibility of using indenters of different geometries. However, the data interpretation for nanoindentation of living cells is often difficult. Despite abundant experimental data reported on nanobiomechanics of living cells, there is a lack of comprehensive discussion on testing with different tip geometries, and the associated mechanical models that enable extracting the mechanical properties of living cells. Therefore, this paper discusses the strategy of selecting the right type of indenter tips and the corresponding mechanical models at given test conditions.
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Affiliation(s)
- Jinju Chen
- School of Mechanical and Systems Engineering, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK
- Arthritis Research UK (ARUK) Tissue Engineering Centre, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
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Lonergan N, Britt L, Sullivan C. Immobilizing live Escherichia coli for AFM studies of surface dynamics. Ultramicroscopy 2014; 137:30-9. [DOI: 10.1016/j.ultramic.2013.10.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 10/23/2013] [Accepted: 10/25/2013] [Indexed: 11/25/2022]
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Günther TJ, Suhr M, Raff J, Pollmann K. Immobilization of microorganisms for AFM studies in liquids. RSC Adv 2014. [DOI: 10.1039/c4ra03874f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Reproducible immobilization method even for living eukaryotes and prokaryotes on polyelectrolyte coated surfaces for high resolution AFM imaging in liquids.
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Affiliation(s)
- Tobias J. Günther
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
| | - Matthias Suhr
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute of Resource Ecology
- 01328 Dresden, Germany
| | - Johannes Raff
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute of Resource Ecology
| | - Katrin Pollmann
- Helmholtz-Zentrum Dresden-Rossendorf
- Institute for Resource Ecology and Helmholtz Institute Freiberg for Resource Technology
- 01328 Dresden, Germany
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27
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Kuyukina MS, Korshunova IO, Rubtsova EV, Ivshina IB. Methods of microorganism immobilization for dynamic atomic-force studies (review). APPL BIOCHEM MICRO+ 2013. [DOI: 10.1134/s0003683814010086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell-cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa.
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29
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Sang S, Zhao Y, Zhang W, Li P, Hu J, Li G. Surface stress-based biosensors. Biosens Bioelectron 2013; 51:124-35. [PMID: 23948243 DOI: 10.1016/j.bios.2013.07.033] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/27/2013] [Accepted: 07/12/2013] [Indexed: 01/13/2023]
Abstract
Surface stress-based biosensors, as one kind of label-free biosensors, have attracted lots of attention in the process of information gathering and measurement for the biological, chemical and medical application with the development of technology and society. This kind of biosensors offers many advantages such as short response time (less than milliseconds) and a typical sensitivity at nanogram, picoliter, femtojoule and attomolar level. Furthermore, it simplifies sample preparation and testing procedures. In this work, progress made towards the use of surface stress-based biosensors for achieving better performance is critically reviewed, including our recent achievement, the optimally circular membrane-based biosensors and biosensor array. The further scientific and technological challenges in this field are also summarized. Critical remark and future steps towards the ultimate surface stress-based biosensors are addressed.
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Affiliation(s)
- Shengbo Sang
- MicroNano System Research Center, Taiyuan University of Technology, Taiyuan, Shanxi 030024, People's Republic of China; Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education, Taiyuan University of Technology, Taiyuan, Shanxi 030024, People's Republic of China
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Dhahri S, Ramonda M, Marlière C. In-situ determination of the mechanical properties of gliding or non-motile bacteria by atomic force microscopy under physiological conditions without immobilization. PLoS One 2013; 8:e61663. [PMID: 23593493 PMCID: PMC3625152 DOI: 10.1371/journal.pone.0061663] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 03/12/2013] [Indexed: 11/19/2022] Open
Abstract
We present a study about AFM imaging of living, moving or self-immobilized bacteria in their genuine physiological liquid medium. No external immobilization protocol, neither chemical nor mechanical, was needed. For the first time, the native gliding movements of Gram-negative Nostoc cyanobacteria upon the surface, at speeds up to 900 µm/h, were studied by AFM. This was possible thanks to an improved combination of a gentle sample preparation process and an AFM procedure based on fast and complete force-distance curves made at every pixel, drastically reducing lateral forces. No limitation in spatial resolution or imaging rate was detected. Gram-positive and non-motile Rhodococcus wratislaviensis bacteria were studied as well. From the approach curves, Young modulus and turgor pressure were measured for both strains at different gliding speeds and are ranging from 20±3 to 105±5 MPa and 40±5 to 310±30 kPa depending on the bacterium and the gliding speed. For Nostoc, spatially limited zones with higher values of stiffness were observed. The related spatial period is much higher than the mean length of Nostoc nodules. This was explained by an inhomogeneous mechanical activation of nodules in the cyanobacterium. We also observed the presence of a soft extra cellular matrix (ECM) around the Nostoc bacterium. Both strains left a track of polymeric slime with variable thicknesses. For Rhodococcus, it is equal to few hundreds of nanometers, likely to promote its adhesion to the sample. While gliding, the Nostoc secretes a slime layer the thickness of which is in the nanometer range and increases with the gliding speed. This result reinforces the hypothesis of a propulsion mechanism based, for Nostoc cyanobacteria, on ejection of slime. These results open a large window on new studies of both dynamical phenomena of practical and fundamental interests such as the formation of biofilms and dynamic properties of bacteria in real physiological conditions.
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Affiliation(s)
- Samia Dhahri
- Géosciences Montpellier, University Montpellier 2, CNRS, Montpellier, France
| | - Michel Ramonda
- Centrale de Technologie en Micro et nanoélectronique, Laboratoire de Microscopie en Champ Proche, University Montpellier 2, Montpellier, France
| | - Christian Marlière
- Géosciences Montpellier, University Montpellier 2, CNRS, Montpellier, France
- Institut des Sciences Moléculaires d'Orsay, University Paris-Sud, CNRS, Orsay, France
- * E-mail:
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31
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Dorobantu LS, Goss GG, Burrell RE. Atomic force microscopy: A nanoscopic view of microbial cell surfaces. Micron 2012; 43:1312-22. [DOI: 10.1016/j.micron.2012.05.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 04/26/2012] [Accepted: 05/11/2012] [Indexed: 11/28/2022]
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32
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Abstract
Unraveling the structure of microbial cells is a major challenge in current microbiology and offers exciting prospects in biomedicine. Atomic force microscopy (AFM) appears as a powerful method to image the surface ultrastructure of live cells under physiological conditions and allows real-time imaging to follow dynamic processes such as cell growth, and division and effects of drugs and chemicals. The following chapter introduces different methods of sample preparation to gain insights into the microbial cell organization. Successful strategies to immobilize microorganisms, including physical entrapment and chemical attachment, are described. This step is a key step and a prerequisite of any analysis and persists as an important limitation to the application of AFM to microbiology due to the wide diversity of microorganisms. Finally, some applications are depicted which underlie the ability of AFM to explore living microbes with unprecedented resolution.
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Krull R, Wucherpfennig T, Esfandabadi ME, Walisko R, Melzer G, Hempel DC, Kampen I, Kwade A, Wittmann C. Characterization and control of fungal morphology for improved production performance in biotechnology. J Biotechnol 2012; 163:112-23. [PMID: 22771505 DOI: 10.1016/j.jbiotec.2012.06.024] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/02/2012] [Accepted: 06/25/2012] [Indexed: 11/25/2022]
Abstract
Filamentous fungi have been widely applied in industrial biotechnology for many decades. In submerged culture processes, they typically exhibit a complex morphological life cycle that is related to production performance--a link that is of high interest for process optimization. The fungal forms can vary from dense spherical pellets to viscous mycelia. The resulting morphology has been shown to be influenced strongly by process parameters, including power input through stirring and aeration, mass transfer characteristics, pH value, osmolality and the presence of solid micro-particles. The surface properties of fungal spores and hyphae also play a role. Due to their high industrial relevance, the past years have seen a substantial development of tools and techniques to characterize the growth of fungi and obtain quantitative estimates on their morphological properties. Based on the novel insights available from such studies, more recent studies have been aimed at the precise control of morphology, i.e., morphology engineering, to produce superior bio-processes with filamentous fungi.
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Affiliation(s)
- Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Germany.
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Perez-Cruz A, Dominguez-Gonzalez A, Stiharu I, Osornio-Rios RA. Optimization of Q-factor of AFM cantilevers using genetic algorithms. Ultramicroscopy 2012; 115:61-7. [DOI: 10.1016/j.ultramic.2012.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 01/18/2012] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
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35
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Osiro D, Filho RB, Assis OBG, Jorge LADC, Colnago LA. Measuring bacterial cells size with AFM. Braz J Microbiol 2012; 43:341-7. [PMID: 24031837 PMCID: PMC3768968 DOI: 10.1590/s1517-838220120001000040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Indexed: 11/22/2022] Open
Abstract
Atomic Force Microscopy (AFM) can be used to obtain high-resolution topographical images of bacteria revealing surface details and cell integrity. During scanning however, the interactions between the AFM probe and the membrane results in distortion of the images. Such distortions or artifacts are the result of geometrical effects related to bacterial cell height, specimen curvature and the AFM probe geometry. The most common artifact in imaging is surface broadening, what can lead to errors in bacterial sizing. Several methods of correction have been proposed to compensate for these artifacts and in this study we describe a simple geometric model for the interaction between the tip (a pyramidal shaped AFM probe) and the bacterium (Escherichia coli JM-109 strain) to minimize the enlarging effect. Approaches to bacteria immobilization and examples of AFM images analysis are also described.
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Affiliation(s)
- Denise Osiro
- Centre Universitârio da Fundaçâo Educacional Guaxupé , Guaxupé, MG , Brasil
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36
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Physico-mechanical characterisation of cells using atomic force microscopy — Current research and methodologies. J Microbiol Methods 2011; 86:131-9. [DOI: 10.1016/j.mimet.2011.05.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/18/2011] [Accepted: 05/26/2011] [Indexed: 11/21/2022]
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37
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Have flagella a preferred orientation during early stages of biofilm formation?: AFM study using patterned substrates. Colloids Surf B Biointerfaces 2011; 82:536-42. [DOI: 10.1016/j.colsurfb.2010.10.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 10/06/2010] [Accepted: 10/07/2010] [Indexed: 11/22/2022]
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38
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Immobilisation of living bacteria for AFM imaging under physiological conditions. Ultramicroscopy 2010; 110:1349-57. [DOI: 10.1016/j.ultramic.2010.06.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 05/18/2010] [Accepted: 06/23/2010] [Indexed: 11/30/2022]
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39
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Jin H, Huang X, Chen Y, Zhao H, Ye H, Huang F, Xing X, Cai J. Photoinactivation effects of hematoporphyrin monomethyl ether on Gram-positive and -negative bacteria detected by atomic force microscopy. Appl Microbiol Biotechnol 2010; 88:761-70. [DOI: 10.1007/s00253-010-2747-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 06/19/2010] [Accepted: 06/20/2010] [Indexed: 10/19/2022]
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40
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Deng Z, Lulevich V, Liu FT, Liu GY. Applications of atomic force microscopy in biophysical chemistry of cells. J Phys Chem B 2010; 114:5971-82. [PMID: 20405961 PMCID: PMC3980964 DOI: 10.1021/jp9114546] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This article addresses the question of what information and new insights atomic force microscopy (AFM) provides that are of importance and relevance to cellular biophysical chemistry research. Three enabling aspects of AFM are discussed: (a) visualization of membrane structural features with nanometer resolution, such as microvilli, ridges, porosomes, lamellapodia, and filopodia; (b) revealing structural evolution associated with cellular signaling pathways by time-dependent and high-resolution imaging of the cellular membrane in correlation with intracellular components from simultaneous optical microscopy; and (c) qualitative and quantitative measurements of single cell mechanics by acquisition of force-deformation profiles and extraction of Young's moduli for the membrane as well as cytoskeleton. A future prospective of AFM is also presented.
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Affiliation(s)
- Zhao Deng
- Department of Chemistry, University of California, Davis, Davis, California 95616
| | - Valentin Lulevich
- Department of Chemistry, University of California, Davis, Davis, California 95616
| | - Fu-tong Liu
- Department of Dermatology, University of California at Davis, Sacramento, California 95817
| | - Gang-yu Liu
- Department of Chemistry, University of California, Davis, Davis, California 95616
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TURNER R, THOMSON N, KIRKHAM J, DEVINE D. Improvement of the pore trapping method to immobilize vital coccoid bacteria for high-resolution AFM: a study ofStaphylococcus aureus. J Microsc 2010; 238:102-10. [DOI: 10.1111/j.1365-2818.2009.03333.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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42
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Wright CJ, Shah MK, Powell LC, Armstrong I. Application of AFM from microbial cell to biofilm. SCANNING 2010; 32:134-49. [PMID: 20648545 DOI: 10.1002/sca.20193] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Atomic Force Microscopy (AFM) has proven itself over recent years as an essential tool for the analysis of microbial systems. This article will review how AFM has been used to study microbial systems to provide unique insight into their behavior and relationship with their environment. Immobilization of live cells has enabled AFM imaging and force measurement to provide understanding of the structure and function of numerous microbial cells. At the macromolecular level AFM investigation into the properties of surface macromolecules and the energies associated with their mechanical conformation and functionality has helped unravel the complex interactions of microbial cells. At the level of the whole cell AFM has provided an integrated analysis of how the microbial cell exploits its environment through its selective, adaptable interface, the cell surface. In addition to these areas of study the AFM investigation of microbial biofilms has been vital for industrial and medical process analysis. There exists a tremendous potential for the future application of AFM to microbial systems and this has been strengthened by the trend to use AFM in combination with other characterization methods, such as confocal microscopy and Raman spectroscopy, to elucidate dynamic cellular processes.
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Affiliation(s)
- Chris J Wright
- Multidisciplinary Nanotechnology Centre, School of Engineering, Swansea University, Swansea, United Kingdom.
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Abstract
Atomic force microscopy (AFM) is a powerful tool for microbiological investigation. This versatile technique cannot only image cellular surfaces at high resolution, but also measure many forms of fundamental interactions over scales ranging from molecules to cells. In this work, we review the recent development of AFM applications in the microbial area. We discuss several approaches for using AFM scanning images to investigate morphological characteristics of microbes and the use of force-distance curves to investigate interaction of microbial samples at the nanometer and cellular levels. Complementary techniques used in combination with AFM for study of microbes are also discussed.
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Affiliation(s)
- Shaoyang Liu
- Biosystems Engineering Department, Auburn University, Auburn, Alabama 36849-5417, USA
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44
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Dorobantu LS, Gray MR. Application of atomic force microscopy in bacterial research. SCANNING 2010; 32:74-96. [PMID: 20695026 DOI: 10.1002/sca.20177] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The atomic force microscope (AFM) has evolved from an imaging device into a multifunctional and powerful toolkit for probing the nanostructures and surface components on the exterior of bacterial cells. Currently, the area of application spans a broad range of interesting fields from materials sciences, in which AFM has been used to deposit patterns of thiol-functionalized molecules onto gold substrates, to biological sciences, in which AFM has been employed to study the undesirable bacterial adhesion to implants and catheters or the essential bacterial adhesion to contaminated soil or aquifers. The unique attribute of AFM is the ability to image bacterial surface features, to measure interaction forces of functionalized probes with these features, and to manipulate these features, for example, by measuring elongation forces under physiological conditions and at high lateral resolution (<1 A). The first imaging studies showed the morphology of various biomolecules followed by rapid progress in visualizing whole bacterial cells. The AFM technique gradually developed into a lab-on-a-tip allowing more quantitative analysis of bacterial samples in aqueous liquids and non-contact modes. Recently, force spectroscopy modes, such as chemical force microscopy, single-cell force spectroscopy, and single-molecule force spectroscopy, have been used to map the spatial arrangement of chemical groups and electrical charges on bacterial surfaces, to measure cell-cell interactions, and to stretch biomolecules. In this review, we present the fascinating options offered by the rapid advances in AFM with emphasizes on bacterial research and provide a background for the exciting research articles to follow.
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Affiliation(s)
- Loredana S Dorobantu
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta, Canada.
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45
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Zhao B, Howard-Knight JP, Humphris ADL, Kailas L, Ratcliffe EC, Foster SJ, Hobbs JK. Large scan area high-speed atomic force microscopy using a resonant scanner. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:093707. [PMID: 19791944 DOI: 10.1063/1.3227238] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A large scan area high-speed scan stage for atomic force microscopy using the resonant oscillation of a quartz bar has been constructed. The sample scanner can be used for high-speed imaging in both air and liquid environments. The well-defined time-position response of the scan stage due to the use of resonance allows highly linearized images to be obtained with a scan size up to 37.5 mum in 0.7 s. The scanner is demonstrated for imaging highly topographic silicon test samples and a semicrystalline polymer undergoing crystallization in air, while images of a polymer and a living bacteria, S. aureus, are obtained in liquid.
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Affiliation(s)
- B Zhao
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield S3 7RH, United Kingdom
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