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Lucidi M, Capecchi G, Visaggio D, Gasperi T, Parisi M, Cincotti G, Rampioni G, Visca P, Kolmakov K. Expanding the microbiologist toolbox via new far-red-emitting dyes suitable for bacterial imaging. Microbiol Spectr 2024; 12:e0369023. [PMID: 38095476 PMCID: PMC10782969 DOI: 10.1128/spectrum.03690-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE By harnessing the versatility of fluorescence microscopy and super-resolution imaging, bacteriologists explore critical aspects of bacterial physiology and resolve bacterial structures sized beyond the light diffraction limit. These techniques are based on fluorophores with profitable photochemical and tagging properties. The paucity of available far-red (FR)-emitting dyes for bacterial imaging strongly limits the multicolor choice of bacteriologists, hindering the possibility of labeling multiple structures in a single experiment. The set of FR fluorophores characterized in this study expands the palette of dyes useful for microbiologists, as they can be used for bacterial LIVE/DEAD staining and for tagging the membranes of viable Escherichia coli and Bacillus subtilis cells. The absence of toxicity makes these dyes suitable for live-cell imaging and allows monitoring of bacterial membrane biogenesis. Moreover, a newly synthesized FR-fluorophore can be employed for imaging bacterial membranes with stimulated emission depletion microscopy, a super-resolution technique capable of increasing the resolving power of conventional microscopes.
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Affiliation(s)
- Massimiliano Lucidi
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | | | - Daniela Visaggio
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Tecla Gasperi
- Department of Science, Roma Tre University, Rome, Italy
| | - Miranda Parisi
- Department of Engineering, University Roma Tre, Rome, Italy
| | | | - Giordano Rampioni
- Department of Science, Roma Tre University, Rome, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Paolo Visca
- Department of Science, Roma Tre University, Rome, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
- IRCCS Fondazione Santa Lucia, Rome, Italy
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2
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Chen X, Xu S, Shabani S, Zhao Y, Fu M, Millis AJ, Fogler MM, Pasupathy AN, Liu M, Basov DN. Machine Learning for Optical Scanning Probe Nanoscopy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2109171. [PMID: 36333118 DOI: 10.1002/adma.202109171] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 07/09/2022] [Indexed: 06/16/2023]
Abstract
The ability to perform nanometer-scale optical imaging and spectroscopy is key to deciphering the low-energy effects in quantum materials, as well as vibrational fingerprints in planetary and extraterrestrial particles, catalytic substances, and aqueous biological samples. These tasks can be accomplished by the scattering-type scanning near-field optical microscopy (s-SNOM) technique that has recently spread to many research fields and enabled notable discoveries. Herein, it is shown that the s-SNOM, together with scanning probe research in general, can benefit in many ways from artificial-intelligence (AI) and machine-learning (ML) algorithms. Augmented with AI- and ML-enhanced data acquisition and analysis, scanning probe optical nanoscopy is poised to become more efficient, accurate, and intelligent.
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Affiliation(s)
- Xinzhong Chen
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
| | - Suheng Xu
- Department of Physics, Columbia University, New York, NY, 10027, USA
| | - Sara Shabani
- Department of Physics, Columbia University, New York, NY, 10027, USA
| | - Yueqi Zhao
- Department of Physics, University of California at San Diego, La Jolla, CA, 92093-0319, USA
| | - Matthew Fu
- Department of Physics, Columbia University, New York, NY, 10027, USA
| | - Andrew J Millis
- Department of Physics, Columbia University, New York, NY, 10027, USA
| | - Michael M Fogler
- Department of Physics, University of California at San Diego, La Jolla, CA, 92093-0319, USA
| | - Abhay N Pasupathy
- Department of Physics, Columbia University, New York, NY, 10027, USA
| | - Mengkun Liu
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY, 11794, USA
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - D N Basov
- Department of Physics, Columbia University, New York, NY, 10027, USA
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3
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Wang J, Peng L, Han D, Zheng T, Chang T, Cui HL. Label-free detection and identification of single bacteria via terahertz near-field imaging. Front Microbiol 2023; 14:1195448. [PMID: 37333650 PMCID: PMC10272414 DOI: 10.3389/fmicb.2023.1195448] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/16/2023] [Indexed: 06/20/2023] Open
Abstract
In recent years, terahertz (THz) imaging has attracted much attention because of its ability to obtain physical and chemical information in a label-free, noninvasive and nonionizing manner. However, the low spatial resolution of traditional THz imaging systems and the weak dielectric response of biological samples hinder the application of this technology in the biomedical field. In this paper, we report a new THz near-field imaging method for a single bacteria, through the coupling effect of nanoscale radius of probe and platinum gold substrate, which greatly enhances THz near-field signal of biological samples. A THz super-resolution image of bacteria has been successfully obtained by strictly controlling the relevant test parameters such as tip parameters and driving amplitude. By analyzing and processing the THz spectral image, the morphology and inner structure of bacteria have been observed. The method has been used to detect and identify Escherichia coli represented by Gram-negative bacteria and Staphylococcus aureus represented by Gram-positive bacteria. This application provides a new label-free, noninvasive and nonionizing testing protocol for the detection of single bacteria.
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Affiliation(s)
- Jie Wang
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Liang Peng
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, China
| | - Dongxue Han
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, China
| | - Teng Zheng
- School of Information and Electrical Engineering, Hangzhou City University, Hangzhou, China
| | - Tianying Chang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hong-Liang Cui
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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4
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Xia F, Youcef-Toumi K. Review: Advanced Atomic Force Microscopy Modes for Biomedical Research. BIOSENSORS 2022; 12:1116. [PMID: 36551083 PMCID: PMC9775674 DOI: 10.3390/bios12121116] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Visualization of biomedical samples in their native environments at the microscopic scale is crucial for studying fundamental principles and discovering biomedical systems with complex interaction. The study of dynamic biological processes requires a microscope system with multiple modalities, high spatial/temporal resolution, large imaging ranges, versatile imaging environments and ideally in-situ manipulation capabilities. Recent development of new Atomic Force Microscopy (AFM) capabilities has made it such a powerful tool for biological and biomedical research. This review introduces novel AFM functionalities including high-speed imaging for dynamic process visualization, mechanobiology with force spectroscopy, molecular species characterization, and AFM nano-manipulation. These capabilities enable many new possibilities for novel scientific research and allow scientists to observe and explore processes at the nanoscale like never before. Selected application examples from recent studies are provided to demonstrate the effectiveness of these AFM techniques.
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5
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Stanciu SG, Tranca DE, Zampini G, Hristu R, Stanciu GA, Chen X, Liu M, Stenmark HA, Latterini L. Scattering-type Scanning Near-Field Optical Microscopy of Polymer-Coated Gold Nanoparticles. ACS OMEGA 2022; 7:11353-11362. [PMID: 35415325 PMCID: PMC8992282 DOI: 10.1021/acsomega.2c00410] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/07/2022] [Indexed: 05/14/2023]
Abstract
Scattering-type scanning near-field optical microscopy (s-SNOM) has emerged over the past years as a powerful characterization tool that can probe important properties of advanced materials and biological samples in a label-free manner, with spatial resolutions lying in the nanoscale realm. In this work, we explore such usefulness in relationship with an interesting class of materials: polymer-coated gold nanoparticles (NPs). As thoroughly discussed in recent works, the interplay between the Au core and the polymeric shell has been found to be important in many applications devoted to biomedicine. We investigate bare Au NPs next to polystyrenesulfonate (PSS) and poly(diallyldimethylammonium chloride) (PDDA) coated ones under 532 nm laser excitation, an wavelength matching the surface plasmon band of the custom-synthesized nanoparticles. We observe consistent s-SNOM phase signals in the case of bare and shallow-coated Au NPs, whereas for thicker shell instances, these signals fade. For all investigated samples, the s-SNOM amplitude signals were found to be very weak, which may be related to reduced scattering efficiency due to absorption of the incident beam. We consider these observations important, as they may facilitate studies and applications in nanomedicine and nanotechnology where the precise positioning of polymer-coated Au NPs with nanoscale resolution is needed besides their dielectric function and related intrinsic optical properties, which are also quantitatively available with s-SNOM.
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Affiliation(s)
- Stefan G. Stanciu
- Center
for Microscopy-Microanalysis and Information Processing, Politehnica University of Bucharest, Bucharest, 060042, Romania
| | - Denis E. Tranca
- Center
for Microscopy-Microanalysis and Information Processing, Politehnica University of Bucharest, Bucharest, 060042, Romania
| | - Giulia Zampini
- Department
of Chemistry, Biology and Biotechnology, Perugia University, Via Elce di sotto, 8, 06123 Perugia, Italy
| | - Radu Hristu
- Center
for Microscopy-Microanalysis and Information Processing, Politehnica University of Bucharest, Bucharest, 060042, Romania
| | - George A. Stanciu
- Center
for Microscopy-Microanalysis and Information Processing, Politehnica University of Bucharest, Bucharest, 060042, Romania
| | - Xinzhong Chen
- Department
of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
| | - Mengkun Liu
- Department
of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, United States
- National
Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Harald A. Stenmark
- Department
of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo 0379, Norway
| | - Loredana Latterini
- Department
of Chemistry, Biology and Biotechnology, Perugia University, Via Elce di sotto, 8, 06123 Perugia, Italy
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6
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Wang H, Xie Q, Xu XG. Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope. Adv Drug Deliv Rev 2022; 180:114080. [PMID: 34906646 DOI: 10.1016/j.addr.2021.114080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/15/2021] [Accepted: 12/06/2021] [Indexed: 11/19/2022]
Abstract
Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.
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Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Xie
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA 18015, USA.
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7
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Infrared nanoscopy and tomography of intracellular structures. Commun Biol 2021; 4:1341. [PMID: 34848821 PMCID: PMC8633277 DOI: 10.1038/s42003-021-02876-7] [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: 07/12/2021] [Accepted: 11/09/2021] [Indexed: 11/08/2022] Open
Abstract
Although techniques such as fluorescence-based super-resolution imaging or confocal microscopy simultaneously gather both morphological and chemical data, these techniques often rely on the use of localized and chemically specific markers. To eliminate this flaw, we have developed a method of examining cellular cross sections using the imaging power of scattering-type scanning near-field optical microscopy and Fourier-transform infrared spectroscopy at a spatial resolution far beyond the diffraction limit. Herewith, nanoscale surface and volumetric chemical imaging is performed using the intrinsic contrast generated by the characteristic absorption of mid-infrared radiation by the covalent bonds. We employ infrared nanoscopy to study the subcellular structures of eukaryotic (Chlamydomonas reinhardtii) and prokaryotic (Escherichia coli) species, revealing chemically distinct regions within each cell such as the microtubular structure of the flagellum. Serial 100 nm-thick cellular cross-sections were compiled into a tomogram yielding a three-dimensional infrared image of subcellular structure distribution at 20 nm resolution. The presented methodology is able to image biological samples complementing current fluorescence nanoscopy but at less interference due to the low energy of infrared radiation and the absence of labeling.
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