1
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Jung P, Zhou X, Iden S, Qu B, Bischoff M. Characterization of the Elasticity of CD4 + T Cells: An Approach Based on Peak Force Quantitative Nanomechanical Mapping. Bio Protoc 2022; 12:e4383. [PMID: 35800101 PMCID: PMC9081480 DOI: 10.21769/bioprotoc.4383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 12/07/2021] [Accepted: 03/02/2022] [Indexed: 12/29/2022] Open
Abstract
CD4+ T cells are essential players in orchestrating the specific immune response against intracellular pathogens, and in inhibiting tumor development in an early stage. The activation of T cells is triggered by engagement of T cell receptors (TCRs). Here, CD3 and CD28 molecules are key factors, (co)stimulating signaling pathways essential for activation and proliferation of CD4+ T cells. T cell activation induces the formation of a tight mechanical bond between T cell and target cell, the so-called immunological synapse (IS). Due to this, mechanical cell properties, including stiffness, play a significant role in modulating cell functions. In the past, many approaches were made to investigate mechanical properties of immune cells, including micropipette aspiration, microplate-based rheometry, techniques based on deformation during cytometry, or the use of optical tweezers. However, the stiffness of T lymphocytes at a subcellular level at the IS still remains largely elusive. With this protocol, we introduce a method based on atomic force microscopy (AFM), to investigate the local cellular stiffness of T cells on functionalized glass/Polydimethylsiloxan (PDMS) surfaces, which mimicks focal stimulation of target cells inducing IS formation by T cells. By applying the peak force nanomechanical mapping (QNM) technique, cellular surface structures and the local stiffness are determined simultaneously, with a resolution of approximately 60 nm. This protocol can be easily adapted to investigate the mechanical impact of numerous factors influencing IS formation and T cell activation. Graphical abstract: Overview of the experimental workflow. Individual experimental steps are shown on the left, hands on and incubation times for each step are shown right.
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Affiliation(s)
- Philipp Jung
- Institute for Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
,
*For correspondence:
| | - Xiangda Zhou
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
| | - Sandra Iden
- Cell and Developmental Biology, Center of Human and Molecular Biology (ZHMB), Saarland University, Homburg, Germany
| | - Bin Qu
- Department of Biophysics, Center for Integrative Physiology and Molecular Medicine (CIPMM), School of Medicine, Saarland University, Homburg, Germany
,Leibniz Institute for New Materials, Saarbrücken, Germany
| | - Markus Bischoff
- Institute for Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
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2
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Moraille P, Abdali Z, Ramkaran M, Polcari D, Patience GS, Dorval Courchesne N, Badia A. Experimental Methods in Chemical Engineering: Atomic force microscopy—
AFM. CAN J CHEM ENG 2022. [DOI: 10.1002/cjce.24407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zahra Abdali
- Chemical Engineering, McGill University Québec Canada
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3
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Gambelli L, Mesman R, Versantvoort W, Diebolder CA, Engel A, Evers W, Jetten MSM, Pabst M, Daum B, van Niftrik L. The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria. Front Microbiol 2021; 12:766527. [PMID: 34925275 PMCID: PMC8671808 DOI: 10.3389/fmicb.2021.766527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/08/2021] [Indexed: 11/25/2022] Open
Abstract
Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.
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Affiliation(s)
- Lavinia Gambelli
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands.,Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Engineering, Mathematics and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - Rob Mesman
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Wouter Versantvoort
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Christoph A Diebolder
- Netherlands Centre for Electron Nanoscopy (NeCEN), Leiden University, Leiden, Netherlands
| | - Andreas Engel
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
| | - Wiel Evers
- Department of Bionanoscience, Delft University of Technology, Delft, Netherlands.,Department of Chemical Engineering, Delft University of Technology, Delft, Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom.,College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Laura van Niftrik
- Department of Microbiology, Faculty of Science, Radboud University, Nijmegen, Netherlands
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4
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Andryukov BG, Karpenko AA, Lyapun IN. Learning from Nature: Bacterial Spores as a Target for Current Technologies in Medicine (Review). Sovrem Tekhnologii Med 2021; 12:105-122. [PMID: 34795986 PMCID: PMC8596247 DOI: 10.17691/stm2020.12.3.13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Indexed: 01/05/2023] Open
Abstract
The capability of some representatives of Clostridium spp. and Bacillus spp. genera to form spores in extreme external conditions long ago became a subject of medico-biological investigations. Bacterial spores represent dormant cellular forms of gram-positive bacteria possessing a high potential of stability and the capability to endure extreme conditions of their habitat. Owing to these properties, bacterial spores are recognized as the most stable systems on the planet, and spore-forming microorganisms became widely spread in various ecosystems. Spore-forming bacteria have been attracted increased interest for years due to their epidemiological danger. Bacterial spores may be in the quiescent state for dozens or hundreds of years but after they appear in the favorable conditions of a human or animal organism, they turn into vegetative forms causing an infectious process. The greatest threat among the pathogenic spore-forming bacteria is posed by the causative agents of anthrax (B. anthracis), food toxicoinfection (B. cereus), pseudomembranous colitis (C. difficile), botulism (C. botulinum), gas gangrene (C. perfringens). For the effective prevention of severe infectious diseases first of all it is necessary to study the molecular structure of bacterial spores and the biochemical mechanisms of sporulation and to develop innovative methods of detection and disinfection of dormant cells. There is another side of the problem: the necessity to investigate exo- and endospores from the standpoint of obtaining similar artificially synthesized models in order to use them in the latest medical technologies for the development of thermostable vaccines, delivery of biologically active substances to the tissues and intracellular structures. In recent years, bacterial spores have become an interesting object for the exploration from the point of view of a new paradigm of unicellular microbiology in order to study microbial heterogeneity by means of the modern analytical tools.
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Affiliation(s)
- B G Andryukov
- Leading Researcher, Laboratory of Molecular Microbiology; G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia; Professor, Department of Fundamental Sciences; Far Eastern Federal University, 10 Village Ayaks, Island Russkiy, Vladivostok, 690922, Russia
| | - A A Karpenko
- Senior Researcher, Laboratory of Cell Biophysics; A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch of the Russian Academy of Sciences, 17 Palchevskogo St., Vladivostok, 690041, Russia
| | - I N Lyapun
- Researcher, Laboratory of Molecular Microbiology G.P. Somov Institute of Epidemiology and Microbiology, 1 Selskaya St., Vladivostok, 690087, Russia
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5
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Shprung T, Wani NA, Wilmes M, Mangoni ML, Bitler A, Shimoni E, Sahl HG, Shai Y. Opposing Effects of PhoPQ and PmrAB on the Properties of Salmonella enterica serovar Typhimurium: Implications on Resistance to Antimicrobial Peptides. Biochemistry 2021; 60:2943-2955. [PMID: 34547893 PMCID: PMC8638962 DOI: 10.1021/acs.biochem.1c00287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The increasing number of resistant
bacteria is a major threat worldwide,
leading to the search for new antibiotic agents. One of the leading
strategies is the use of antimicrobial peptides (AMPs), cationic and
hydrophobic innate immune defense peptides. A major target of AMPs
is the bacterial membrane. Notably, accumulating data suggest that
AMPs can activate the two-component systems (TCSs) of Gram-negative
bacteria. These include PhoP-PhoQ (PhoPQ) and PmrA-PmrB (PmrAB), responsible
for remodeling of the bacterial cell surface. To better understand
this mechanism, we utilized bacteria deficient either in one system
alone or in both and biophysical tools including fluorescence spectroscopy,
single-cell atomic force microscopy, electron microscopy, and mass
spectrometry (MoskowitzS. M.;Antimicrob. Agents Chemother.2012, 56, 1019−103022106224; ChengH. Y.;J. Biomed. Sci.2010, 17, 6020653976). Our data suggested that the two systems have opposing
effects on the properties of Salmonella enterica. The knockout of PhoPQ made the bacteria more susceptible to AMPs
by making the surface less rigid, more polarized, and permeable with
a slightly more negatively charged cell wall. In addition, the periplasmic
space is thinner. In contrast, the knockout of PmrAB did not affect
its susceptibility, while it made the bacterial outer layer very rigid,
less polarized, and less permeable than the other two mutants, with
a negatively charged cell wall similar to the WT. Overall, the data
suggest that the coexistence of systems with opposing effects on the
biophysical properties of the bacteria contribute to their membrane
flexibility, which, on the one hand, is important to accommodate changing
environments and, on the other hand, may inhibit the development of
meaningful resistance to AMPs.
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Affiliation(s)
- Tal Shprung
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Naiem Ahmad Wani
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Miriam Wilmes
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Maria Luisa Mangoni
- Department of Biochemical Sciences A. Rossi Fanelli, Faculty of Pharmacy and Medicine, Sapienza University of Rome, CU27, 00185 Roma, Italy
| | - Arkadi Bitler
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal Shimoni
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hans-Georg Sahl
- Pharmaceutical Microbiology Section, Institute for Medical Microbiology, Immunology and Parasitology, University of Bonn, Sigmund-Freud-Strasse 25, D-53127 Bonn, Germany
| | - Yechiel Shai
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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6
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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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7
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Bashiri S, Lucidi M, Visaggio D, Capecchi G, Persichetti L, Cincotti G, Visca P, Capellini G. Growth Phase- and Desiccation-Dependent Acinetobacter baumannii Morphology: An Atomic Force Microscopy Investigation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1110-1119. [PMID: 33433226 DOI: 10.1021/acs.langmuir.0c02980] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Acinetobacter baumannii has emerged as a major bacterial pathogen during the past three decades. The majority of the A. baumannii infections occur in hospitals and are caused by strains endowed with high desiccation tolerance, which represents an essential feature for the adaptation to the nosocomial environment. This work aims at investigating the desiccation response of the multidrug-resistant A. baumannii strain ACICU as a function of the bacterial growth phase and oxygen availability, by correlating bacterial survival with shape alterations. The three-dimensional morphological analysis of bacteria was carried out by atomic force microscopy (AFM), following the evolution of bacterial shape descriptors, such as the area, volume, roughness of individual cell membranes, and the cell cluster roughness, which exhibited peculiar and distinctive behavior as a function of the growth conditions. AFM images of A. baumannii ACICU cells revealed the prevalence of the coccoid morphology at all growth stages, with a tendency to reduce their size in the stationary phase, accompanied by a higher survival rate to air-drying. Moreover, cells harvested from the logarithmic phase featured a larger volume and resulted to be more sensitive to desiccation compared to the cells harvested at later growth stages. In addition, oxygen deprivation caused a significant decrease in cellular size and was associated with the formation of pores in the cell membrane, accompanied by a relative reduction in culturability after desiccation. Morphological plasticity and multidrug resistance may contribute to desiccation tolerance and therefore to persistence in the hospital setting.
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Affiliation(s)
- Shadi Bashiri
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Massimiliano Lucidi
- Department of Engineering, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Daniela Visaggio
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Giulia Capecchi
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Luca Persichetti
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Gabriella Cincotti
- Department of Engineering, University Roma Tre, via Vito Volterra 62, 00146 Rome, Italy
| | - Paolo Visca
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
| | - Giovanni Capellini
- Department of Science, University Roma Tre, viale Guglielmo Marconi 446, 00146 Rome, Italy
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8
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Ruiz-Rincón S, González-Orive A, Grazú V, Fratila RM, Fuente JMDL, Cea P. Altering model cell membranes by means of localized magnetic heating. Colloids Surf B Biointerfaces 2020; 196:111315. [PMID: 32818926 DOI: 10.1016/j.colsurfb.2020.111315] [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: 01/21/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 10/23/2022]
Abstract
Isolated iron oxide magnetic nanoparticles (MNPs), 12 nm in diameter, coated with oleic acid molecules as capping agents have been deposited by the Langmuir-Blodgett (LB) method onto a model cell membrane incorporating 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and Cholesterol (Chol) in the 1:1 ratio, which was also fabricated by the LB technique. Atomic Force Microscopy (AFM) experiments showed that the application of an alternating magnetic field results in the embedding of the MNPs through the phospholipidic layer. These experimental results reveal that the heating of individual MNPs may induce a local increase in the fluidity of the film with a large control of the spatial and temporal specificity.
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Affiliation(s)
- Silvia Ruiz-Rincón
- Instituto de Nanociencia de Aragón (INA), Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain; Laboratorio de Microscopias Avanzadas (LMA),Campus Río Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain; Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alejandro González-Orive
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Strasse 100, 33098 Paderborn, Germany
| | - Valeria Grazú
- Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain; Networking Biomedical Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Raluca M Fratila
- Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain; Networking Biomedical Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Jesús M de la Fuente
- Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain; Networking Biomedical Research Centre of Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Spain
| | - Pilar Cea
- Instituto de Nanociencia de Aragón (INA), Campus Rio Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain; Laboratorio de Microscopias Avanzadas (LMA),Campus Río Ebro, Universidad de Zaragoza, C/Mariano Esquillor, s/n, 50018 Zaragoza, Spain; Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain; Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza, 50009, Zaragoza, Spain.
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9
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Salavadhi SS, Chintalapani S, Ramachandran R, Nagubandi K, Ramisetti A, Boyapati R. Atomic Force Microscopy: A three-dimensional reconstructive tool of oral microbiota in gingivitis and periodontitis. J Indian Soc Periodontol 2018; 21:264-269. [PMID: 29456299 PMCID: PMC5813339 DOI: 10.4103/jisp.jisp_209_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: This study aims to ascertain the advantages of Atomic Force Microscopy (AFM) in the morphologic study of microorganisms and their interactions within the subgingival biofilm in patients with gingivitis and periodontitis. Settings and Design: Conducted a study on twenty patients, ten patients with severe periodontitis with probing the pocket depth of ≥8 mm, with a clinical attachment loss (CAL) of ≥6 mm CAL and ten patients with gingivitis: ≥5 mm pocket depth, and no attachment loss, was selected for the study. Materials and Methods: Bacterial biofilms were collected and slide preparation done. Morphological study was done using AFM. AFM consists of a cantilever-mounted tip, a piezoelectric scanner, a photodetector diode, a laser diode, and a feedback control. The laser beam is reflected from back of the cantilever into the quadrant of the photodetector. AFM works on the principle of interaction between the tip and the sample which causes the cantilever to deflect, thereby changing the position of laser onto the photodetector. Methodology used for studying the bacteria through AFM includes the following: (1) Probe type: Platinum coated silicon nitrate tip. (2) Probe force: 0.11 N/m. (3) Probe geometry: Triangular shaped tip. (4) Probe frequency: 22 KHz. (5) Probe immobilization: Used in Contact mode. AFM Solver Pro-M (NT-MDT) equipped with ETALON probe was used to take images in Nova software. Results: The investigation showed various morphological features, such as shape, size, and secretory product-like vesicles of the bacterial species involved in gingivitis and periodontitis. More bacterial surface details were studied by reproducing a three-dimensional reconstruction using AFM. Conclusions: The morphological variations of bacteria of different sizes, and shapes, cell wall structures, secretory product-like vesicles flagellated and filamentous microorganisms, polymorphonuclear leukocytes, and bacterial coaggregation analysis were done by AFM. Results of the present study conclude that AFM is a quite a reliable method for studying morphology of bacterial species involving periodontal diseases and is also used to study microbial interactions in biofilm.
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Affiliation(s)
| | | | | | | | - Arpita Ramisetti
- Department of Periodontics, Mamata Dental College, Khammam, Telangana, India
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10
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Nautiyal P, Alam F, Balani K, Agarwal A. The Role of Nanomechanics in Healthcare. Adv Healthc Mater 2018; 7. [PMID: 29193838 DOI: 10.1002/adhm.201700793] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/18/2017] [Indexed: 12/21/2022]
Abstract
Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.
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Affiliation(s)
- Pranjal Nautiyal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
| | - Fahad Alam
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Kantesh Balani
- Biomaterials Processing and Characterization Laboratory Department of Materials Science and Engineering Indian Institute of Technology Kanpur Kanpur 208016 India
| | - Arvind Agarwal
- Nanomechanics and Nanotribology Laboratory Florida International University 10555 West Flagler Street Miami FL 33174 USA
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11
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Uchihashi T, Scheuring S. Applications of high-speed atomic force microscopy to real-time visualization of dynamic biomolecular processes. Biochim Biophys Acta Gen Subj 2018; 1862:229-240. [DOI: 10.1016/j.bbagen.2017.07.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/13/2017] [Indexed: 12/12/2022]
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12
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Lyubchenko YL. Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:403001. [PMID: 30410191 PMCID: PMC6217977 DOI: 10.1088/1361-6463/aad898] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.
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Affiliation(s)
- Yuri L Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
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13
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Li M, Dang D, Xi N, Wang Y, Liu L. Nanoscale imaging and force probing of biomolecular systems using atomic force microscopy: from single molecules to living cells. NANOSCALE 2017; 9:17643-17666. [PMID: 29135007 DOI: 10.1039/c7nr07023c] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Due to the lack of adequate tools for observation, native molecular behaviors at the nanoscale have been poorly understood. The advent of atomic force microscopy (AFM) provides an exciting instrument for investigating physiological processes on individual living cells with molecular resolution, which attracts the attention of worldwide researchers. In the past few decades, AFM has been widely utilized to investigate molecular activities on diverse biological interfaces, and the performances and functions of AFM have also been continuously improved, greatly improving our understanding of the behaviors of single molecules in action and demonstrating the important role of AFM in addressing biological issues with unprecedented spatiotemporal resolution. In this article, we review the related techniques and recent progress about applying AFM to characterize biomolecular systems in situ from single molecules to living cells. The challenges and future directions are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang 110016, China.
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14
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Iturri J, Toca-Herrera JL. Characterization of Cell Scaffolds by Atomic Force Microscopy. Polymers (Basel) 2017; 9:E383. [PMID: 30971057 PMCID: PMC6418519 DOI: 10.3390/polym9080383] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 08/13/2017] [Accepted: 08/16/2017] [Indexed: 12/12/2022] Open
Abstract
This review reports on the use of the atomic force microscopy (AFM) in the investigation of cell scaffolds in recent years. It is shown how the technique is able to deliver information about the scaffold surface properties (e.g., topography), as well as about its mechanical behavior (Young's modulus, viscosity, and adhesion). In addition, this short review also points out the utilization of the atomic force microscope technique beyond its usual employment in order to investigate another type of basic questions related to materials physics, chemistry, and biology. The final section discusses in detail the novel uses that those alternative measuring modes can bring to this field in the future.
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Affiliation(s)
- Jagoba Iturri
- Institute for Biophysics, Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Wien, Austria.
| | - José L Toca-Herrera
- Institute for Biophysics, Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Wien, Austria.
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15
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Ruiz-Rincón S, González-Orive A, de la Fuente JM, Cea P. Reversible Monolayer-Bilayer Transition in Supported Phospholipid LB Films under the Presence of Water: Morphological and Nanomechanical Behavior. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:7538-7547. [PMID: 28691823 DOI: 10.1021/acs.langmuir.7b01268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mixed monolayer Langmuir-Blodgett (LB) films of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol (Chol) in the 1:1 ratio have been prepared onto solid mica substrates. Upon immersion in water or in an aqueous HEPES solution (pH 7.4) the monolayer LB films were spontaneously converted into well-organized bilayers leaving free mica areas. The process has been demonstrated to be reversible upon removal of the aqueous solution, resulting in remarkably free of defects monolayers that are homogeneously distributed onto the mica. In addition, the nanomechanical properties exhibited by the as-formed bilayers have been determined by means of AFM breakthrough force studies. The bilayers formed by immersion of the monolayer in an aqueous media exhibit nanomechanical properties and stability under compression analogous to those of DPPC:Chol supported bilayers obtained by other methods previously described in the literature. Consequently, the hydration of a monolayer LB film has been revealed as an easy method to produce well-ordered bilayers that mimic the cell membrane and that could be used as model cell membranes.
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Affiliation(s)
| | | | - Jesús M de la Fuente
- Instituto de Ciencia de Materiales de Aragón (ICMA), Universidad de Zaragoza-CSIC , 50009 Zaragoza, Spain
- Networking Biomedical Research Center of Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Zaragoza, Spain
| | - Pilar Cea
- Departamento de Química Física, Facultad de Ciencias, Universidad de Zaragoza , 50009, Zaragoza, Spain
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16
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Neri-Bazán RM, García-Machorro J, Méndez-Luna D, Tolentino-López LE, Martínez-Ramos F, Padilla-Martínez II, Aguilar-Faisal L, Soriano-Ursúa MA, Trujillo-Ferrara JG, Fragoso-Vázquez MJ, Barrón BL, Correa-Basurto J. Design, in silico studies, synthesis and in vitro evaluation of oseltamivir derivatives as inhibitors of neuraminidase from influenza A virus H1N1. Eur J Med Chem 2017; 128:154-167. [PMID: 28182988 DOI: 10.1016/j.ejmech.2017.01.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/22/2016] [Accepted: 01/23/2017] [Indexed: 02/07/2023]
Abstract
Since the neuraminidase (NA) enzyme of the influenza A virus plays a key role in the process of release of new viral particles from a host cell, it is often a target for new drug design. The emergence of NA mutations, such as H275Y, has led to great resistance against neuraminidase inhibitors, including oseltamivir and zanamivir. Hence, we herein designed a set of derivatives by modifying the amine and/or carboxylic groups of oseltamivir. After being screened for their physicochemical (Lipinski's rule) and toxicological properties, the remaining compounds were submitted to molecular and theoretical studies. The docking simulations provided insights into NA recognition patterns, demonstrating that oseltamivir modified at the carboxylic moiety and coupled with anilines had higher affinity and a better binding pose for NA than the derivatives modified at the amine group. Based on these theoretical studies, the new oseltamivir derivatives may have higher affinity to mutant variants and possibly to other viral subtypes. Accordingly, two compounds were selected for synthesis, which together with their respective intermediates were evaluated for their cytotoxicity and antiviral activities. Their biological activity was then tested in cells infected with the A/Puerto Rico/916/34 (H1N1) influenza virus, and virus yield reduction assays were performed. Additionally, by measuring neuraminidase activity with the neuraminidase assay kit it was found that the compounds produced inhibitory activity on this enzyme. Finally, the infected cells were analysed with atomic force microscopy (AFM), observing morphological changes strongly suggesting that these compounds interfered with cellular release of viral particles.
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Affiliation(s)
- Rocío M Neri-Bazán
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Jazmín García-Machorro
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico.
| | - David Méndez-Luna
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Luis E Tolentino-López
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Federico Martínez-Ramos
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - Itzia I Padilla-Martínez
- Departamento de Ciencia Básica, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto s/n., Barrio La Laguna Ticomán, 07340, Mexico
| | - Leopoldo Aguilar-Faisal
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - Marvin A Soriano-Ursúa
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - José G Trujillo-Ferrara
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico
| | - M Jonathan Fragoso-Vázquez
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - Blanca L Barrón
- Laboratorio de Investigación, Departamento de Química Inorgánica, Departamento de Química Orgánica, Laboratorio de Virología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala s/n, Col. Santo Tomas, 11340, Mexico
| | - José Correa-Basurto
- Laboratorios de Modelado Molecular y Diseño de Fármacos, Bioquímica, Medicina de Conservación, Fisiología, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional Plan de San Luis y Díaz Mirón s/n, 11340, Mexico.
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17
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Edwards DT, Perkins TT. Optimizing force spectroscopy by modifying commercial cantilevers: Improved stability, precision, and temporal resolution. J Struct Biol 2017; 197:13-25. [DOI: 10.1016/j.jsb.2016.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/13/2016] [Accepted: 01/18/2016] [Indexed: 11/24/2022]
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18
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Mularski A, Separovic F. Atomic Force Microscopy Studies of the Interaction of Antimicrobial Peptides with Bacterial Cells. Aust J Chem 2017. [DOI: 10.1071/ch16425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Antimicrobial peptides (AMPs) are promising therapeutic alternatives to conventional antibiotics. Many AMPs are membrane-active but their mode of action in killing bacteria or in inhibiting their growth remains elusive. Recent studies indicate the mechanism of action depends on peptide structure and lipid components of the bacterial cell membrane. Owing to the complexity of working with living cells, most of these studies have been conducted with synthetic membrane systems, which neglect the possible role of bacterial surface structures in these interactions. In recent years, atomic force microscopy has been utilized to study a diverse range of biological systems under non-destructive, physiologically relevant conditions that yield in situ biophysical measurements of living cells. This approach has been applied to the study of AMP interaction with bacterial cells, generating data that describe how the peptides modulate various biophysical behaviours of individual bacteria, including the turgor pressure, cell wall elasticity, bacterial capsule thickness, and organization of bacterial adhesins.
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Gumí-Audenis B, Costa L, Carlá F, Comin F, Sanz F, Giannotti MI. Structure and Nanomechanics of Model Membranes by Atomic Force Microscopy and Spectroscopy: Insights into the Role of Cholesterol and Sphingolipids. MEMBRANES 2016; 6:E58. [PMID: 27999368 PMCID: PMC5192414 DOI: 10.3390/membranes6040058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/12/2016] [Accepted: 12/14/2016] [Indexed: 11/17/2022]
Abstract
Biological membranes mediate several biological processes that are directly associated with their physical properties but sometimes difficult to evaluate. Supported lipid bilayers (SLBs) are model systems widely used to characterize the structure of biological membranes. Cholesterol (Chol) plays an essential role in the modulation of membrane physical properties. It directly influences the order and mechanical stability of the lipid bilayers, and it is known to laterally segregate in rafts in the outer leaflet of the membrane together with sphingolipids (SLs). Atomic force microscope (AFM) is a powerful tool as it is capable to sense and apply forces with high accuracy, with distance and force resolution at the nanoscale, and in a controlled environment. AFM-based force spectroscopy (AFM-FS) has become a crucial technique to study the nanomechanical stability of SLBs by controlling the liquid media and the temperature variations. In this contribution, we review recent AFM and AFM-FS studies on the effect of Chol on the morphology and mechanical properties of model SLBs, including complex bilayers containing SLs. We also introduce a promising combination of AFM and X-ray (XR) techniques that allows for in situ characterization of dynamic processes, providing structural, morphological, and nanomechanical information.
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Affiliation(s)
- Berta Gumí-Audenis
- Nanoprobes and Nanoswitches group, Institute for Bioengineering of Catalunya (IBEC), Barcelona 08028, Spain.
- Physical Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain.
- European Synchrotron Radiation Facility (ESRF), Grenoble 38043, France.
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28028, Spain.
| | - Luca Costa
- Structure and Dynamics of Nucleoproteic and Membrane Assemblies, Centre de Biochimie Structurale (CBS), Montpellier 34090, France.
| | - Francesco Carlá
- European Synchrotron Radiation Facility (ESRF), Grenoble 38043, France.
| | - Fabio Comin
- European Synchrotron Radiation Facility (ESRF), Grenoble 38043, France.
| | - Fausto Sanz
- Nanoprobes and Nanoswitches group, Institute for Bioengineering of Catalunya (IBEC), Barcelona 08028, Spain.
- Physical Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain.
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28028, Spain.
| | - Marina I Giannotti
- Nanoprobes and Nanoswitches group, Institute for Bioengineering of Catalunya (IBEC), Barcelona 08028, Spain.
- Physical Chemistry Department, Universitat de Barcelona, Barcelona 08028, Spain.
- Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid 28028, Spain.
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20
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Feng J, Lamour G, Xue R, Mirvakliki MN, Hatzikiriakos SG, Xu J, Li H, Wang S, Lu X. Chemical, physical and morphological properties of bacterial biofilms affect survival of encased Campylobacter jejuni F38011 under aerobic stress. Int J Food Microbiol 2016; 238:172-182. [PMID: 27648759 DOI: 10.1016/j.ijfoodmicro.2016.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/22/2016] [Accepted: 09/11/2016] [Indexed: 11/18/2022]
Abstract
Campylobacter jejuni is a microaerophilic pathogen and leading cause of human gastroenteritis. The presence of C. jejuni encased in biofilms found in meat and poultry processing facilities may be the major strategy for its survival and dissemination in aerobic environment. In this study, Staphylococcus aureus, Salmonella enterica, or Pseudomonas aeruginosa was mixed with C. jejuni F38011 as a culture to form dual-species biofilms. After 4days' exposure to aerobic stress, no viable C. jejuni cells could be detected from mono-species C. jejuni biofilm. In contrast, at least 4.7logCFU/cm2 of viable C. jejuni cells existed in some dual-species biofilms. To elucidate the mechanism of protection mode, chemical, physical and morphological features of biofilms were characterized. Dual-species biofilms contained a higher level of extracellular polymeric substances with a more diversified chemical composition, especially for polysaccharides and proteins, than mono-species C. jejuni biofilm. Structure of dual-species biofilms was more compact and their surface was >8 times smoother than mono-species C. jejuni biofilm, as indicated by atomic force microscopy. Under desiccation stress, water content of dual-species biofilms decreased slowly and remained at higher levels for a longer time than mono-species C. jejuni biofilm. The surface of all biofilms was hydrophilic, but total surface energy of dual-species biofilms (ranging from 52.5 to 56.2mJ/m2) was lower than that of mono-species C. jejuni biofilm, leading to more resistance to wetting by polar liquids. This knowledge can aid in developing intervention strategies to decrease the survival and dispersal of C. jejuni into foods or environment.
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Affiliation(s)
- Jinsong Feng
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Guillaume Lamour
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Rui Xue
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mehr Negar Mirvakliki
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Savvas G Hatzikiriakos
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Jie Xu
- Department of Mechanical and Industrial Engineering, University of Illinois at Chicago, Chicago, IL 60607, United States
| | - Hongbin Li
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Shuo Wang
- Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xiaonan Lu
- Food, Nutrition, and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
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Hodel AW, Leung C, Dudkina NV, Saibil HR, Hoogenboom BW. Atomic force microscopy of membrane pore formation by cholesterol dependent cytolysins. Curr Opin Struct Biol 2016; 39:8-15. [DOI: 10.1016/j.sbi.2016.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/08/2016] [Accepted: 03/14/2016] [Indexed: 11/16/2022]
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22
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Conjugated gold nanoparticles as a tool for probing the bacterial cell envelope: The case of Shewanella oneidensis MR-1. Biointerphases 2016; 11:011003. [PMID: 26746161 DOI: 10.1116/1.4939244] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The bacterial cell envelope forms the interface between the interior of the cell and the outer world and is, thus, the means of communication with the environment. In particular, the outer cell surface mediates the adhesion of bacteria to the surface, the first step in biofilm formation. While a number of ligand-based interactions are known for the attachment process in commensal organisms and, as a result, opportunistic pathogens, the process of nonspecific attachment is thought to be mediated by colloidal, physiochemical, interactions. It is becoming clear, however, that colloidal models ignore the heterogeneity of the bacterial surface, and that the so-called nonspecific attachment may be mediated by specific regions of the cell surface, whether or not the relevant interaction is ligand-mediate. The authors introduce surface functionalized gold nanoparticles to probe the surface chemistry of Shewanella oneidensis MR-1 as it relates to surface attachment to ω-substituted alkanethiolates self-assembled monolayers (SAMs). A linear relationship between the attachment of S. oneidensis to SAM modified planar substrates and the number of similarly modified nanoparticles attached to the bacterial surfaces was demonstrated. In addition, the authors demonstrate that carboxylic acid-terminated nanoparticles attach preferentially to the subpolar region of the S. oneidensis and obliteration of that binding preference corresponds in loss of attachment to carboxylic acid terminated SAMs. Moreover, this region corresponds to suspected functional regions of the S. oneidensis surface. Because this method can be employed over large numbers of cells, this method is expected to be generally applicable for understanding cell surface organization across populations.
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23
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Applications of Atomic Force Microscopy in Exploring Drug Actions in Lymphoma-Targeted Therapy at the Nanoscale. BIONANOSCIENCE 2016. [DOI: 10.1007/s12668-015-0180-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
This article reviews atomic force microscopy (AFM) studies of DNA structure and dynamics and protein-DNA complexes, including recent advances in the visualization of protein-DNA complexes with the use of cutting-edge, high-speed AFM. Special emphasis is given to direct nanoscale visualization of dynamics of protein-DNA complexes. In the area of DNA structure and dynamics, structural studies of local non-B conformations of DNA and the interplay of local and global DNA conformations are reviewed. The application of time-lapse AFM nanoscale imaging of DNA dynamics is illustrated by studies of Holliday junction branch migration. Structure and dynamics of protein-DNA interactions include problems related to site-specific DNA recombination, DNA replication, and DNA mismatch repair. Studies involving the structure and dynamics of chromatin are also described.
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Affiliation(s)
- Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
| | - Luda S. Shlyakhtenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025
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25
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Loskill P, Pereira PM, Jung P, Bischoff M, Herrmann M, Pinho MG, Jacobs K. Reduction of the peptidoglycan crosslinking causes a decrease in stiffness of the Staphylococcus aureus cell envelope. Biophys J 2015; 107:1082-1089. [PMID: 25185544 DOI: 10.1016/j.bpj.2014.07.029] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/30/2014] [Accepted: 07/15/2014] [Indexed: 11/28/2022] Open
Abstract
We have used atomic-force microscopy (AFM) to probe the effect of peptidoglycan crosslinking reduction on the elasticity of the Staphylococcus aureus cell wall, which is of particular interest as a target for antimicrobial chemotherapy. Penicillin-binding protein 4 (PBP4) is a nonessential transpeptidase, required for the high levels of peptidoglycan crosslinking characteristic of S. aureus. Importantly, this protein is essential for β-lactam resistance in community-acquired, methicillin-resistant S. aureus (MRSA) strains but not in hospital-acquired MRSA strains. Using AFM in a new mode for recording force/distance curves, we observed that the absence of PBP4, and the concomitant reduction of the peptidoglycan crosslinking, resulted in a reduction in stiffness of the S. aureus cell wall. Importantly, the reduction in cell wall stiffness in the absence of PBP4 was observed both in community-acquired and hospital-acquired MRSA strains, indicating that high levels of peptidoglycan crosslinking modulate the overall structure and mechanical properties of the S. aureus cell envelope in both types of clinically relevant strains. Additionally, we were able to show that the applied method enables the separation of cell wall properties and turgor pressure.
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Affiliation(s)
- Peter Loskill
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Pedro M Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Philipp Jung
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
| | - Karin Jacobs
- Experimental Physics, Saarland University, Saarbrücken, Germany.
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Gumí-Audenis B, Sanz F, Giannotti MI. Impact of galactosylceramides on the nanomechanical properties of lipid bilayer models: an AFM-force spectroscopy study. SOFT MATTER 2015; 11:5447-5454. [PMID: 26058499 DOI: 10.1039/c5sm01252j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Galactosylceramides (GalCer) are glycosphingolipids bound to a monosaccharide group, responsible for inducing extensive hydrogen bonds that yield their alignment and accumulation in the outer leaflet of the biological membrane together with cholesterol (Chol) in rafts. In this work, the influence of GalCer on the nanomechanical properties of supported lipid bilayers (SLBs) based on DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and DLPC (1,2-didodecanoyl-sn-glycero-3-phosphocoline) as model systems was assessed. Phosphatidylcholine (PC):GalCer SLBs were characterized by means of differential scanning calorimetry (DSC) and atomic force microscopy (AFM), in both imaging and force spectroscopy (AFM-FS) modes. Comparing both PC systems, we determined that the behaviour of SLB mixtures is governed by the PC phase-like state at the working temperature. While a phase segregated system is observed for DLPC:GalCer SLBs, GalCer are found to be dissolved in DPPC SLBs for GalCer contents up to 20 mol%. In both systems, the incorporation of GalCer intensifies the nanomechanical properties of SLBs. Interestingly, segregated domains of exceptionally high mechanical stability are formed in DLPC:GalCer SLBs. Finally, the role of 20 mol% Chol in GalCer organization and function in the membranes was assessed. Both PC model systems displayed phase segregation and remarkable nanomechanical stability when GalCer and Chol coexist in SLBs.
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Affiliation(s)
- Berta Gumí-Audenis
- Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac 10-12, Barcelona, 08028, Spain.
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27
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Haase K, Pelling AE. Investigating cell mechanics with atomic force microscopy. J R Soc Interface 2015; 12:20140970. [PMID: 25589563 PMCID: PMC4345470 DOI: 10.1098/rsif.2014.0970] [Citation(s) in RCA: 216] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/18/2014] [Indexed: 12/12/2022] Open
Abstract
Transmission of mechanical force is crucial for normal cell development and functioning. However, the process of mechanotransduction cannot be studied in isolation from cell mechanics. Thus, in order to understand how cells 'feel', we must first understand how they deform and recover from physical perturbations. Owing to its versatility, atomic force microscopy (AFM) has become a popular tool to study intrinsic cellular mechanical properties. Used to directly manipulate and examine whole and subcellular reactions, AFM allows for top-down and reconstitutive approaches to mechanical characterization. These studies show that the responses of cells and their components are complex, and largely depend on the magnitude and time scale of loading. In this review, we generally describe the mechanotransductive process through discussion of well-known mechanosensors. We then focus on discussion of recent examples where AFM is used to specifically probe the elastic and inelastic responses of single cells undergoing deformation. We present a brief overview of classical and current models often used to characterize observed cellular phenomena in response to force. Both simple mechanistic models and complex nonlinear models have been used to describe the observed cellular behaviours, however a unifying description of cell mechanics has not yet been resolved.
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Affiliation(s)
- Kristina Haase
- Department of Physics, Centre for Interdisciplinary NanoPhysics, MacDonald Hall, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario, Canada
| | - Andrew E Pelling
- Department of Physics, Centre for Interdisciplinary NanoPhysics, MacDonald Hall, University of Ottawa, 150 Louis Pasteur, Ottawa, Ontario, Canada Department of Biology, Gendron Hall, 30 Marie Curie, University of Ottawa, Ottawa, Ontario, Canada Institute for Science Society and Policy, Desmarais Building, 55 Laurier Ave. East, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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Palusinska-Szysz M, Zdybicka-Barabas A, Cytryńska M, Wdowiak-Wróbel S, Chmiel E, Gruszecki WI. Analysis of cell surface alterations in Legionella pneumophila cells treated with human apolipoprotein E. Pathog Dis 2015; 73:1-8. [PMID: 25176171 DOI: 10.1111/2049-632x.12214] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Binding of human apolipoprotein E (apoE) to Legionella pneumophila lipopolysaccharide was analysed at the molecular level by Fourier-transform infrared spectroscopy, thereby providing biophysical evidence for apoE-L. pneumophila lipopolysaccharide interaction. Atomic force microscopy imaging of apoE-exposed L. pneumophila cells revealed alterations in the bacterial cell surface topography and nanomechanical properties in comparison with control bacteria. The changes induced by apoE binding to lipopolysaccharide on the surface of L. pneumophila cells may participate in: (1) impeding the penetration of host cells by the bacteria; (2) suppression of pathogen intracellular growth and eventually; and (3) inhibition of the development of infection.
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Affiliation(s)
- Marta Palusinska-Szysz
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Agnieszka Zdybicka-Barabas
- Department of Immunobiology, Institute of Biology and Biochemistry, Maria Curie-Sklodowska University, Lublin, Poland
| | - Małgorzata Cytryńska
- Department of Immunobiology, Institute of Biology and Biochemistry, Maria Curie-Sklodowska University, Lublin, Poland
| | - Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Elżbieta Chmiel
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Sklodowska University, Lublin, Poland
| | - Wiesław I Gruszecki
- Department of Biophysics, Institute of Physics, Maria Curie-Sklodowska University, Lublin, Poland
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29
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Hu X, Dinu CZ. Analysis of affinities between specific biological ligands using atomic force microscopy. Analyst 2015; 140:8118-26. [PMID: 26525901 DOI: 10.1039/c5an01748c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We used atomic force microscopy to rank the energetics of biomolecular recognition events of protein–ligand complexes.
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Affiliation(s)
- Xiao Hu
- West Virginia University
- Department of Chemical Engineering
- Morgantown
- USA
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30
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Burgain J, Scher J, Francius G, Borges F, Corgneau M, Revol-Junelles A, Cailliez-Grimal C, Gaiani C. Lactic acid bacteria in dairy food: surface characterization and interactions with food matrix components. Adv Colloid Interface Sci 2014; 213:21-35. [PMID: 25277266 DOI: 10.1016/j.cis.2014.09.005] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 08/30/2014] [Accepted: 09/01/2014] [Indexed: 02/07/2023]
Abstract
This review gives an overview of the importance of interactions occurring in dairy matrices between Lactic Acid Bacteria and milk components. Dairy products are important sources of biological active compounds of particular relevance to human health. These compounds include immunoglobulins, whey proteins and peptides, polar lipids, and lactic acid bacteria including probiotics. A better understanding of interactions between bioactive components and their delivery matrix may successfully improve their transport to their target site of action. Pioneering research on probiotic lactic acid bacteria has mainly focused on their host effects. However, very little is known about their interaction with dairy ingredients. Such knowledge could contribute to designing new and more efficient dairy food, and to better understand relationships between milk constituents. The purpose of this review is first to provide an overview of the current knowledge about the biomolecules produced on bacterial surface and the composition of the dairy matter. In order to understand how bacteria interact with dairy molecules, adhesion mechanisms are subsequently reviewed with a special focus on the environmental conditions affecting bacterial adhesion. Methods dedicated to investigate the bacterial surface and to decipher interactions between bacteria and abiotic dairy components are also detailed. Finally, relevant industrial implications of these interactions are presented and discussed.
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31
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Benitez R, Toca-herrera JL. Looking at cell mechanics with atomic force microscopy: Experiment and theory. Microsc Res Tech 2014; 77:947-58. [DOI: 10.1002/jemt.22419] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 07/24/2014] [Accepted: 07/25/2014] [Indexed: 11/08/2022]
Affiliation(s)
- Rafael Benitez
- Department of Mathematics; University Center of Plasencia, University of Extremadura, Avda. Virgen del Puerto 2; 10600 Plasencia Spain
| | - José. L. Toca-herrera
- Institute for Biophysics, Department of Nanobiotechnology; University of Natural Resources and Life Sciences Vienna (BOKU), Muthgasse 11; 1190 Vienna Austria
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32
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Wu N, Wang Q, Zhou X, Jia SS, Fan Y, Hu J, Li B. Probing tethered targets of a single biomolecular complex with atomic force microscopy. J Mol Recognit 2014; 26:700-4. [PMID: 24277616 DOI: 10.1002/jmr.2338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 09/29/2013] [Accepted: 10/24/2013] [Indexed: 12/29/2022]
Abstract
DNA origami shows tremendous promise as templates for the assembly of nano-components and detection of molecular recognition events. So far, the method of choice for evaluating these structures has been atomic force microscopy (AFM), a powerful tool for imaging nanoscale objects. In most cases, tethered targets on DNA origami have proven to be highly effective samples for investigation. Still, while maximal assembly of the nanostructures might benefit from the greatest flexibility in the tether, AFM imaging requires a sufficient stability of the adsorbed components. The balance between the tether flexibility and sample stability is a major, poorly understood, concern in such studies. Here, we investigated the dependence of the tethering length on molecular capture events monitored by AFM. In our experiments, single biotin molecules were attached to DNA origami templates with various linker lengths of thymidine nucleotides, and their interaction with streptavidin was observed with AFM. Our results show that the streptavidin-biotin complexes are easily detected with short tethered lengths, and that their morphological features clearly change with the tethering length. We identify the functionally useful tether lengths for these investigations, which are also expected to prove useful in the construction and further application of DNA origami in bio-nanotechnology studies.
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Affiliation(s)
- Na Wu
- Division of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201800, China
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33
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Kainz B, Oprzeska-Zingrebe EA, Herrera JL. Biomaterial and cellular properties as examined through atomic force microscopy, fluorescence optical microscopies and spectroscopic techniques. Biotechnol J 2013; 9:51-60. [DOI: 10.1002/biot.201300087] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 09/23/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
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34
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Lima LMC, Giannotti MI, Redondo-Morata L, Vale MLC, Marques EF, Sanz F. Morphological and nanomechanical behavior of supported lipid bilayers on addition of cationic surfactants. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9352-61. [PMID: 23782267 DOI: 10.1021/la400067n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The addition of surfactants to lipid bilayers is important for the modulation of lipid bilayer properties (e.g., in protein reconstitution and development of nonviral gene delivery vehicles) and to provide insight on the properties of natural biomembranes. In this work, the thermal behavior, organization, and nanomechanical stability of model cationic lipid-surfactant bilayers have been investigated. Two different cationic surfactants, hexadecyltrimethylammonium bromide (CTAB) and a novel derivative of the amino acid serine (Ser16TFAc), have been added (up to 50 mol %) to both liposomes and supported lipid bilayers (SLBs) composed by the zwitterionic phospholipid DPPC. The thermal phase behavior of mixed liposomes has been probed by differential scanning calorimetry (DSC), and the morphology and nanomechanical properties of mixed SLBs by atomic force microscopy-based force spectroscopy (AFM-FS). Although DSC thermograms show different results for the two mixed liposomes, when both are deposited on mica substrates similar trends on the morphology and the mechanical response of the lipid-surfactant bilayers are observed. DSC thermograms indicate microdomain formation in both systems, but while CTAB decreases the degree of organization on the liposome bilayer, Ser16TFAc ultimately induces the opposite effect. Regarding the AFM-FS studies, they show that microphase segregation occurs for these systems and that the effect is dependent on the surfactant content. In both SLB systems, different microdomains characterized by their height and breakthrough force Fb are formed. The molecular organization and composition is critically discussed in the light of our experimental results and literature data on similar lipid-surfactant systems.
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Affiliation(s)
- Lia M C Lima
- Centro de Investigação em Química, Department of Chemistry and Biochemistry, University of Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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35
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Antimicrobial peptide trichokonin VI-induced alterations in the morphological and nanomechanical properties of Bacillus subtilis. PLoS One 2012; 7:e45818. [PMID: 23049870 PMCID: PMC3458079 DOI: 10.1371/journal.pone.0045818] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
Antimicrobial peptides are promising alternative antimicrobial agents compared to conventional antibiotics. Understanding the mode of action is important for their further application. We examined the interaction between trichokonin VI, a peptaibol isolated from Trichoderma pseudokoningii, and Bacillus subtilis, a representative Gram-positive bacterium. Trichokonin VI was effective against B. subtilis with a minimal inhibitory concentration of 25 µM. Trichokonin VI exhibited a concentration- and time-dependent effect against B. subtilis, which was studied using atomic force microscopy. The cell wall of B. subtilis collapsed and the roughness increased upon treatment with trichokonin VI. Nanoindentation experiments revealed a progressive decrease in the stiffness of the cells. Furthermore, the membrane permeabilization effect of trichokonin VI on B. subtilis was monitored, and the results suggest that the leakage of intracellular materials is a possible mechanism of action for trichokonin VI, which led to alterations in the morphological and nanomechanical properties of B. subtilis.
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36
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Redondo-Morata L, Giannotti MI, Sanz F. Influence of cholesterol on the phase transition of lipid bilayers: a temperature-controlled force spectroscopy study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12851-12860. [PMID: 22873775 DOI: 10.1021/la302620t] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cholesterol (Chol) plays the essential function of regulating the physical properties of the cell membrane by controlling the lipid organization and phase behavior and, thus, managing the membrane fluidity and its mechanical strength. Here, we explore the model system DPPC:Chol by means of temperature-controlled atomic force microscopy (AFM) imaging and AFM-based force spectroscopy (AFM-FS) to assess the influence of Chol on the membrane ordering and stability. We analyze the system in a representative range of compositions up to 50 mol % Chol studying the phase evolution upon temperature increase (from room temperature to temperatures high above the T(m) of the DPPC bilayer) and the corresponding (nano)mechanical stability. By this means, we correlate the mechanical behavior and composition with the lateral order of each phase present in the bilayers. We prove that low Chol contents lead to a phase-segregated system, whereas high contents of Chol can give a homogeneous bilayer. In both cases, Chol enhances the mechanical stability of the membrane, and an extraordinarily stable system is observed for equimolar fractions (50 mol % Chol). In addition, even when no thermal transition is detected by the traditional bulk analysis techniques for liposomes with high Chol content (40 and 50 mol %), we demonstrate that temperature-controlled AFM-FS is capable of identifying a thermal transition for the supported lipid bilayers. Finally, our results validate the AFM-FS technique as an ideal platform to differentiate phase coexistence and transitions in lipid bilayers and bridge the gap between the results obtained by traditional methods for bulk analysis, the theoretical predictions, and the behavior of these systems at the nanoscale.
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Affiliation(s)
- Lorena Redondo-Morata
- Institute for Bioengineering of Catalonia (IBEC), Baldiri i Reixac 15-21, 08028, Barcelona, Spain
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37
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Yamashita H, Taoka A, Uchihashi T, Asano T, Ando T, Fukumori Y. Single-Molecule Imaging on Living Bacterial Cell Surface by High-Speed AFM. J Mol Biol 2012; 422:300-9. [DOI: 10.1016/j.jmb.2012.05.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/14/2012] [Indexed: 11/27/2022]
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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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39
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Arnal L, Serra DO, Cattelan N, Castez MF, Vázquez L, Salvarezza RC, Yantorno OM, Vela ME. Adhesin contribution to nanomechanical properties of the virulent Bordetella pertussis envelope. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:7461-7469. [PMID: 22515332 DOI: 10.1021/la300811m] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Adherence to a biological surface allows bacteria to colonize and persist within the host and represents an essential first step in the pathogenesis of most bacterial diseases. Consequently, the physicochemical properties of the outer membrane in bacteria play a key role for attachment to surfaces and therefore for biofilm formation. Bordetella pertussis is a Gram-negative bacterium that colonizes the respiratory tract of humans, producing whooping cough or pertussis, a highly infectious disease. B. pertussis uses various adhesins exposed on its surface to promote cell-surface and cell-cell interactions. The most dominant adhesin function is displayed by filamentous hemagglutinin (FHA). B. pertussis Tohama I wild-type (Vir+) strain and two defective mutants, an avirulent (Vir-) and a FHA-deficient (FHA-) B. pertussis strains were studied by AFM under physiological conditions to evaluate how the presence or absence of adhesins affects the mechanical properties of the B. pertussis cell surface. Quantitative information on the nanomechanical properties of the bacterial envelope was obtained by AFM force-volume analysis. These studies suggested that the presence of virulence factors is correlated with an increase in the average membrane rigidity, which is largely influenced by the presence of FHA. Moreover, for this system we built a nanoscale stiffness map that reveals an inhomogeneous spatial distribution of Young modulus as well as the presence of rigid nanodomains on the cell surface.
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Affiliation(s)
- L Arnal
- Facultad de Ciencias Exactas, Centro de Investigación y Desarrollo de Fermentaciones Industriales (CINDEFI-CONICET-CCT La Plata), UNLP. 50 No. 227, 1900 La Plata, Argentina
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40
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Redondo-Morata L, Giannotti MI, Sanz F. AFM-based force-clamp monitors lipid bilayer failure kinetics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:6403-6410. [PMID: 22443887 DOI: 10.1021/la3005147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The lipid bilayer rupture phenomenon is here explored by means of atomic force microscopy (AFM)-based force clamp, for the first time to our knowledge, to evaluate how lipid membranes respond when compressed under an external constant force, in the range of nanonewtons. Using this method, we were able to directly quantify the kinetics of the membrane rupture event and the associated energy barriers, for both single supported bilayers and multibilayers, in contradistinction to the classic studies performed at constant velocity. Moreover, the affected area of the membrane during the rupture process was calculated using an elastic deformation model. The elucidated information not only contributes to a better understanding of such relevant process, but also proves the suitability of AFM-based force clamp to study model structures as lipid bilayers. These findings on the kinetics of lipid bilayers rupture could be extended and applied to the study of other molecular thin films. Furthermore, systems of higher complexity such as models mimicking cell membranes could be studied by means of AFM-based force-clamp technique.
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Affiliation(s)
- Lorena Redondo-Morata
- Institute for Bioengineering of Catalonia (IBEC), 15-21 Baldiri I Reixac, 08028 Barcelona, Spain
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41
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Characterization of bacterial polysaccharide capsules and detection in the presence of deliquescent water by atomic force microscopy. Appl Environ Microbiol 2012; 78:3476-9. [PMID: 22344657 DOI: 10.1128/aem.00207-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We detected polysaccharide capsules from Zunongwangia profunda SM-A87 with atomic force microscopy (AFM). The molecular organization of the capsules at the single-polysaccharide-chain level was reported. Furthermore, we found that with ScanAsyst mode the polysaccharide capsules could be detected even in the presence of deliquescent water covering the capsule.
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42
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Tripathi P, Dupres V, Beaussart A, Lebeer S, Claes IJJ, Vanderleyden J, Dufrêne YF. Deciphering the nanometer-scale organization and assembly of Lactobacillus rhamnosus GG pili using atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2211-2216. [PMID: 22149133 DOI: 10.1021/la203834d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In living cells, sophisticated functional interfaces are generated through the self-assembly of bioactive building blocks. Prominent examples of such biofunctional surfaces are bacterial nanostructures referred to as pili. Although these proteinaceous filaments exhibit remarkable structure and functions, their potential to design bioinspired self-assembled systems has been overlooked. Here, we used atomic force microscopy (AFM) to explore the supramolecular organization and self-assembly of pili from the Gram-positive probiotic bacterium Lactobacillus rhamnosus GG (LGG). High-resolution AFM imaging of cell preparations adsorbed on mica revealed pili not only all around the cells, but also in the form of remarkable star-like structures assembled on the mica surface. Next, we showed that two-step centrifugation is a simple procedure to separate large amounts of pili, even though through their synthesis they are covalently anchored to the cell wall. We also found that the centrifuged pili assemble as long bundles. We suggest that these bundles originate from a complex interplay of mechanical effects (centrifugal force) and biomolecular interactions involving the SpaC cell adhesion pilin subunit (lectin-glycan bonds, hydrophobic bonds). Supporting this view, we found that pili isolated from an LGG mutant lacking hydrophilic exopolysaccharides show an increased tendency to form tight bundles. These experiments demonstrate that AFM is a powerful platform for visualizing individual pili on bacterial surfaces and for unravelling their two-dimensional assembly on solid surfaces. Our data suggest that bacterial pili may provide a generic approach in nanobiotechnology for elaborating functional supramolecular interfaces assembled from bioactive building blocks.
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Affiliation(s)
- Prachi Tripathi
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Croix du Sud 2/18, B-1348 Louvain-la-Neuve, Belgium
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43
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From the regulation of peptidoglycan synthesis to bacterial growth and morphology. Nat Rev Microbiol 2011; 10:123-36. [PMID: 22203377 DOI: 10.1038/nrmicro2677] [Citation(s) in RCA: 869] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
How bacteria grow and divide while retaining a defined shape is a fundamental question in microbiology, but technological advances are now driving a new understanding of how the shape-maintaining bacterial peptidoglycan sacculus grows. In this Review, we highlight the relationship between peptidoglycan synthesis complexes and cytoskeletal elements, as well as recent evidence that peptidoglycan growth is regulated from outside the sacculus in Gram-negative bacteria. We also discuss how growth of the sacculus is sensitive to mechanical force and nutritional status, and describe the roles of peptidoglycan hydrolases in generating cell shape and of D-amino acids in sacculus remodelling.
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44
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Soon RL, Nation RL, Harper M, Adler B, Boyce JD, Tan CH, Li J, Larson I. Effect of colistin exposure and growth phase on the surface properties of live Acinetobacter baumannii cells examined by atomic force microscopy. Int J Antimicrob Agents 2011; 38:493-501. [PMID: 21925844 DOI: 10.1016/j.ijantimicag.2011.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 07/20/2011] [Accepted: 07/26/2011] [Indexed: 11/17/2022]
Abstract
The diminishing antimicrobial development pipeline has forced the revival of colistin as a last line of defence against infections caused by multidrug-resistant Gram-negative 'superbugs' such as Acinetobacter baumannii. The complete loss of lipopolysaccharide (LPS) mediates colistin resistance in some A. baumannii strains. Atomic force microscopy was used to examine the surface properties of colistin-susceptible and -resistant A. baumannii strains at mid-logarithmic and stationary growth phases in liquid and in response to colistin treatment. The contribution of LPS to surface properties was investigated using A. baumannii strains constructed with and without the lpxA gene. Bacterial spring constant measurements revealed that colistin-susceptible cells were significantly stiffer than colistin-resistant cells at both growth phases (P<0.01), whilst colistin treatment at high concentrations (32 mg/L) resulted in more rigid surfaces for both phenotypes. Multiple, large adhesive peaks frequently noted in force curves captured on colistin-susceptible cells were not evident for colistin-resistant cells. Adhesion events were markedly reduced following colistin exposure. The cell membranes of strains of both phenotypes remained intact following colistin treatment, although fine topographical details were illustrated. These studies, conducted for the first time on live A. baumannii cells in liquid, have contributed to our understanding of the action of colistin in this problematic pathogen.
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Affiliation(s)
- Rachel L Soon
- Facility for Anti-infective Drug Development and Innovation, Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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45
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Milani P, Gholamirad M, Traas J, Arnéodo A, Boudaoud A, Argoul F, Hamant O. In vivo analysis of local wall stiffness at the shoot apical meristem in Arabidopsis using atomic force microscopy. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 67:1116-23. [PMID: 21605208 DOI: 10.1111/j.1365-313x.2011.04649.x] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Whereas the morphogenesis of developing organisms is relatively well understood at the molecular level, the contribution of the mechanical properties of the cells to shape changes remains largely unknown, mainly because of the lack of quantified biophysical parameters at cellular or subcellular resolution. Here we designed an atomic force microscopy approach to investigate the elastic modulus of the outer cell wall in living shoot apical meristems (SAMs). SAMs are highly organized structures that contain the plant stem cells, and generate all of the aerial organs of the plant. Building on modeling and experimental data, we designed a protocol that is able to measure very local properties, i.e. within 40-100 nm deep into the wall of living meristematic cells. We identified three levels of complexity at the meristem surface, with significant heterogeneity in stiffness at regional, cellular and even subcellular levels. Strikingly, we found that the outer cell wall was much stiffer at the tip of the meristem (5 ± 2 MPa on average), covering the stem cell pool, than on the flanks of the meristem (1.5 ± 0.7 MPa on average). Altogether, these results demonstrate the existence of a multiscale spatialization of the mechanical properties of the meristem surface, in addition to the previously established molecular and cytological zonation of the SAM, correlating with regional growth rate distribution.
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Affiliation(s)
- Pascale Milani
- Laboratoire Joliot Curie, Laboratoire de Physique, CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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46
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Zdybicka-Barabas A, Januszanis B, Mak P, Cytryńska M. An atomic force microscopy study of Galleria mellonella apolipophorin III effect on bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1896-906. [DOI: 10.1016/j.bbamem.2011.03.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Revised: 03/17/2011] [Accepted: 03/22/2011] [Indexed: 11/24/2022]
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47
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Statistical analysis of long- and short-range forces involved in bacterial adhesion to substratum surfaces as measured using atomic force microscopy. Appl Environ Microbiol 2011; 77:5065-70. [PMID: 21642399 DOI: 10.1128/aem.00502-11] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Surface thermodynamic analyses of microbial adhesion using measured contact angles on solid substrata and microbial cell surfaces are widely employed to determine the nature of the adhesion forces, i.e., the interplay between Lifshitz-van der Waals and acid-base forces. While surface thermodynamic analyses are often viewed critically, atomic force microscopy (AFM) can also provide information on the nature of the adhesion forces by means of Poisson analysis of the measured forces. This review first presents a description of Poisson analysis and its underlying assumptions. The data available from the literature for different combinations of bacterial strains and substrata are then summarized, leading to the conclusion that bacterial adhesion to surfaces is generally dominated by short-range, attractive acid-base interactions, in combination with long-range, weaker Lifshitz-van der Waals forces. This is in line with the findings of surface thermodynamic analyses of bacterial adhesion. Comparison with single-molecule ligand-receptor forces from the literature suggests that the short-range-force contribution from Poisson analysis involves a discrete adhesive bacterial cell surface site rather than a single molecular force. The adhesion force arising from these cell surface sites and the number of sites available may differ from strain to strain. Force spectroscopy, however, involves the tedious task of identifying the minor peaks in the AFM retraction force-distance curve. This step can be avoided by carrying out Poisson analysis on the work of adhesion, which can also be derived from retraction force-distance curves. This newly proposed way of performing Poisson analysis confirms that multiple molecular bonds, rather than a single molecular bond, contribute to a discrete adhesive bacterial cell surface site.
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Liou JW, Gu MH, Chen YK, Chen WY, Chen YC, Tseng YH, Hung YJ, Chang HH. Visible light responsive photocatalyst induces progressive and apical-terminus preferential damages on Escherichia coli surfaces. PLoS One 2011; 6:e19982. [PMID: 21589873 PMCID: PMC3093399 DOI: 10.1371/journal.pone.0019982] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Accepted: 04/22/2011] [Indexed: 01/10/2023] Open
Abstract
Background Recent research shows that visible-light responsive photocatalysts have potential usage in antimicrobial applications. However, the dynamic changes in the damage to photocatalyzed bacteria remain unclear. Methodology/Principal Findings Facilitated by atomic force microscopy, this study analyzes the visible-light driven photocatalyst-mediated damage of Escherichia coli. Results show that antibacterial properties are associated with the appearance of hole-like structures on the bacteria surfaces. Unexpectedly, these hole-like structures were preferentially induced at the apical terminus of rod shaped E. coli cells. Differentiating the damages into various levels and analyzing the percentage of damage to the cells showed that photocatalysis was likely to elicit sequential damages in E. coli cells. The process began with changing the surface properties on bacterial cells, as indicated in surface roughness measurements using atomic force microscopy, and holes then formed at the apical terminus of the cells. The holes were then subsequently enlarged until the cells were totally transformed into a flattened shape. Parallel experiments indicated that photocatalysis-induced bacterial protein leakage is associated with the progression of hole-like damages, further suggesting pore formation. Control experiments using ultraviolet light responsive titanium-dioxide substrates also obtained similar observations, suggesting that this is a general phenomenon of E. coli in response to photocatalysis. Conclusion/Significance The photocatalysis-mediated localization-preferential damage to E. coli cells reveals the weak points of the bacteria. This might facilitate the investigation of antibacterial mechanism of the photocatalysis.
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Affiliation(s)
- Je-Wen Liou
- Department of Biochemistry, Tzu Chi University, Hualien, Taiwan, Republic of China
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan, Republic of China
- Nanotechnology Research Center, National Dong-Hwa University, Hualien, Taiwan, Republic of China
| | - Ming-Hui Gu
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Yen-Kai Chen
- Department of Biochemistry, Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Wen-Yi Chen
- Department of Biochemistry, Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Yi-Cheng Chen
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan, Republic of China
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Yao-Hsuan Tseng
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan, Republic of China
| | - Yu-Jiun Hung
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan, Republic of China
| | - Hsin-Hou Chang
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan, Republic of China
- Nanotechnology Research Center, National Dong-Hwa University, Hualien, Taiwan, Republic of China
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, Taiwan, Republic of China
- * E-mail:
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Abstract
Modern microbiological research has increasingly focused on the interactions between bacterial cells and the surfaces that they inhabit. To this end, microfluidic devices have played a large role in enabling research of cell-surface interactions, especially surface attachment and biofilm formation. This review provides background on microfluidic devices and their use in biological systems, as well specific examples from current literature. Methods to observe and interrogate cells within microfluidic devices are described, as well as the analytical techniques that are used to collect these data.
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Affiliation(s)
- Aaron P Mosier
- College of Nanoscale Science and Engineering (CNSE), University at Albany, Albany, NY, USA.
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Abstract
Gram-negative bacteria and mitochondria are both covered by two distinct biological membranes. These membrane systems have been maintained during the course of evolution from an early evolutionary precursor. Both outer membranes accommodate channels of the porin family, which are designed for the uptake and exchange of metabolites, including ions and small molecules, such as nucleosides or sugars. In bacteria, the structure of the outer membrane porin protein family of β-barrels is generally characterized by an even number of β-strands; usually 14, 16 or 18 strands are observed forming the bacterial porin barrel wall. In contrast, the recent structures of the mitochondrial porin, also known as VDAC (voltage-dependent anion channel), show an uneven number of 19 β-strands, but a similar molecular architecture. Despite the lack of a clear evolutionary link between these protein families, their common principles and differences in assembly, architecture and function are summarized in the present review.
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