101
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Francis AT, Shears MJ, Murphy SC, Fu D. Direct Quantification of Single Red Blood Cell Hemoglobin Concentration with Multiphoton Microscopy. Anal Chem 2020; 92:12235-12241. [PMID: 32786430 DOI: 10.1021/acs.analchem.0c01609] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood disorders, diseases, and infections often affect the shape, number, and content of red blood cells (RBCs) dramatically. To combat these pathologies, many therapies target RBCs and their contents directly. Mean corpuscular hemoglobin concentration (MCHC) is an important pathological metric in both identification and treatment. However, current methods for RBC analysis and MCHC quantification rely on bulk measurements. Single RBC measurements could provide necessary insight into the heterogeneity of RBC health and improve therapeutic efficacy. In this study, we present a novel multimodal multiphoton approach for quantifying hemoglobin concentration at single RBC resolution. We achieve this by collecting two images simultaneously that allows us to excite water with stimulated Raman scattering and hemoglobin with transient absorption. This multimodal imaging is enabled by a newly designed orthogonal modulation theme for dual-channel lock-in detection. By leveraging water as an internal standard, we quantify MCHC of healthy RBCs and RBCs infected with Plasmodium yoelii, a commonly studied rodent parasite model.
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Affiliation(s)
- Andrew T Francis
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Melanie J Shears
- Department of Laboratory Medicine and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Sean C Murphy
- Department of Laboratory Medicine and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, 750 Republican Street, Seattle, Washington 98109, United States
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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102
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Strbkova L, Carson BB, Vincent T, Vesely P, Chmelik R. Automated interpretation of time-lapse quantitative phase image by machine learning to study cellular dynamics during epithelial-mesenchymal transition. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200024R. [PMID: 32812412 PMCID: PMC7431880 DOI: 10.1117/1.jbo.25.8.086502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
SIGNIFICANCE Machine learning is increasingly being applied to the classification of microscopic data. In order to detect some complex and dynamic cellular processes, time-resolved live-cell imaging might be necessary. Incorporating the temporal information into the classification process may allow for a better and more specific classification. AIM We propose a methodology for cell classification based on the time-lapse quantitative phase images (QPIs) gained by digital holographic microscopy (DHM) with the goal of increasing performance of classification of dynamic cellular processes. APPROACH The methodology was demonstrated by studying epithelial-mesenchymal transition (EMT) which entails major and distinct time-dependent morphological changes. The time-lapse QPIs of EMT were obtained over a 48-h period and specific novel features representing the dynamic cell behavior were extracted. The two distinct end-state phenotypes were classified by several supervised machine learning algorithms and the results were compared with the classification performed on single-time-point images. RESULTS In comparison to the single-time-point approach, our data suggest the incorporation of temporal information into the classification of cell phenotypes during EMT improves performance by nearly 9% in terms of accuracy, and further indicate the potential of DHM to monitor cellular morphological changes. CONCLUSIONS Proposed approach based on the time-lapse images gained by DHM could improve the monitoring of live cell behavior in an automated fashion and could be further developed into a tool for high-throughput automated analysis of unique cell behavior.
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Affiliation(s)
- Lenka Strbkova
- Brno University of Technology, Central European Institute of Technology, Brno, Czech Republic
| | - Brittany B. Carson
- Uppsala University, Department of Immunology, Genetics, and Pathology (IGP), Rudbeck Laboratory, Uppsala, Sweden
| | - Theresa Vincent
- Uppsala University, Department of Immunology, Genetics, and Pathology (IGP), Rudbeck Laboratory, Uppsala, Sweden
- NYU School of Medicine, Department of Microbiology, New York, United States
| | - Pavel Vesely
- Brno University of Technology, Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno, Czech Republic
| | - Radim Chmelik
- Brno University of Technology, Institute of Physical Engineering, Faculty of Mechanical Engineering, Brno, Czech Republic
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103
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Matanfack GA, Taubert M, Guo S, Houhou R, Bocklitz T, Küsel K, Rösch P, Popp J. Influence of Carbon Sources on Quantification of Deuterium Incorporation in Heterotrophic Bacteria: A Raman-Stable Isotope Labeling Approach. Anal Chem 2020; 92:11429-11437. [DOI: 10.1021/acs.analchem.0c02443] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Shuxia Guo
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
| | - Rola Houhou
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
| | - Thomas Bocklitz
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
| | - Kirsten Küsel
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology (Leibniz-IPHT), Albert-Einstein-Straße 9, 07745 Jena, Germany
- Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
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104
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Shi L, Gayen T, Budansky Y, Yoo K, Secor J, Harvey T, Harvey G, Shumyatsky P, Nolan D, Alfano R. Enhanced stimulated raman scattering of solvent due to anharmonic energy transfer from resonance raman solute molecules. OPTICS EXPRESS 2020; 28:21792-21804. [PMID: 32752451 PMCID: PMC7470682 DOI: 10.1364/oe.395406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 06/15/2020] [Indexed: 05/19/2023]
Abstract
A new nonlinear optical process, named enhanced stimulated Raman scattering (ESRS), is reported for the first time from resonance Raman in β-carotene-methanol solution. It is well known that absorption decreases the efficiency of the nonlinear optical and laser processes; however, we observed enhanced stimulated Raman peaks at the first and second Stokes from methanol solvent at 2834 cm-1 with the addition of β-carotene solutes. This enhanced SRS effect in methanol is attributed to the resonance Raman (RR) process in β-carotene, which creates a significant number of vibrations from RR and the excess vibrations are transferred to methanol from anharmonic vibrational interactions between the β-carotene solutes and the methanol solvent, and consequently leads to the increased Raman gain.
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Affiliation(s)
- Lingyan Shi
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Lingyan Shi and Taposh Gayen contributed equally
| | - Taposh Gayen
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
- Lingyan Shi and Taposh Gayen contributed equally
| | - Yury Budansky
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
| | - Kerr Yoo
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
| | - Jeff Secor
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
| | | | | | - Pavel Shumyatsky
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
| | - Daniel Nolan
- Corning Inc., One Riverfront Plaza, Corning, NY 14831, USA
| | - Robert Alfano
- Institute of Ultrafast Spectroscopy and Lasers, the City College of New York, NY 10031, USA
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105
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Shi L, Liu X, Shi L, Stinson HT, Rowlette J, Kahl LJ, Evans CR, Zheng C, Dietrich LEP, Min W. Mid-infrared metabolic imaging with vibrational probes. Nat Methods 2020; 17:844-851. [PMID: 32601425 PMCID: PMC7396315 DOI: 10.1038/s41592-020-0883-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 05/27/2020] [Indexed: 02/06/2023]
Abstract
Understanding metabolism is indispensable in unraveling the mechanistic basis of many physiological and pathological processes. However, in situ metabolic imaging tools are still lacking. Here we introduce a framework for mid-infrared (MIR) metabolic imaging by coupling the emerging high-information-throughput MIR microscopy with specifically designed IR-active vibrational probes. We present three categories of small vibrational tags including azide bond, 13C-edited carbonyl bond and deuterium-labeled probes to interrogate various metabolic activities in cells, small organisms and mice. Two MIR imaging platforms are implemented including broadband Fourier transform infrared microscopy and discrete frequency infrared microscopy with a newly incorporated spectral region (2,000-2,300 cm-1). Our technique is uniquely suited to metabolic imaging with high information throughput. In particular, we performed single-cell metabolic profiling including heterogeneity characterization, and large-area metabolic imaging at tissue or organ level with rich spectral information.
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Affiliation(s)
- Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Xinwen Liu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lingyan Shi
- Department of Chemistry, Columbia University, New York, NY, USA.,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | | | | | - Lisa J Kahl
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | | | - Chaogu Zheng
- Department of Biological Sciences, Columbia University, New York, NY, USA.,School of Biological Science, The University of Hong Kong, Hong Kong, China
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA. .,Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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106
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Spectroscopic coherent Raman imaging of Caenorhabditis elegans reveals lipid particle diversity. Nat Chem Biol 2020; 16:1087-1095. [PMID: 32572275 DOI: 10.1038/s41589-020-0565-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
Caenorhabditis elegans serves as a model for understanding adiposity and its connections to aging. Current methodologies do not distinguish between fats serving the energy needs of the parent, akin to mammalian adiposity, from those that are distributed to the progeny, making it difficult to accurately interpret the physiological implications of fat content changes induced by external perturbations. Using spectroscopic coherent Raman imaging, we determine the protein content, chemical profiles and dynamics of lipid particles in live animals. We find fat particles in the adult intestine to be diverse, with most destined for the developing progeny. In contrast, the skin-like epidermis contains fats that are the least heterogeneous, the least dynamic and have high triglyceride content. These attributes are most consistent with stored somatic energy reservoirs. These results challenge the prevailing practice of assessing C. elegans adiposity by measurements that are dominated by the intestinal fat content.
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107
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Xiong H, Qian N, Zhao Z, Shi L, Miao Y, Min W. Background-free imaging of chemical bonds by a simple and robust frequency-modulated stimulated Raman scattering microscopy. OPTICS EXPRESS 2020; 28:15663-15677. [PMID: 32403589 PMCID: PMC7340375 DOI: 10.1364/oe.391016] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 05/21/2023]
Abstract
Being able to image chemical bonds with high sensitivity and speed, stimulated Raman scattering (SRS) microscopy has made a major impact in biomedical optics. However, it is well known that the standard SRS microscopy suffers from various backgrounds, limiting the achievable contrast, quantification and sensitivity. While many frequency-modulation (FM) SRS schemes have been demonstrated to retrieve the sharp vibrational contrast, they often require customized laser systems and/or complicated laser pulse shaping or introduce additional noise, thereby hindering wide adoption. Herein we report a simple but robust strategy for FM-SRS microscopy based on a popular commercial laser system and regular optics. Harnessing self-phase modulation induced self-balanced spectral splitting of picosecond Stokes beam propagating in standard single-mode silica fibers, a high-performance FM-SRS system is constructed without introducing any additional signal noise. Our strategy enables adaptive spectral resolution for background-free SRS imaging of Raman modes with different linewidths. The generality of our method is demonstrated on a variety of Raman modes with effective suppressing of backgrounds including non-resonant cross phase modulation and electronic background from two-photon absorption or pump-probe process. As such, our method is promising to be adopted by the SRS microscopy community for background-free chemical imaging.
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Affiliation(s)
- Hanqing Xiong
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Naixin Qian
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Lingyan Shi
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Yupeng Miao
- Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10032, USA
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108
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Eicosapentaenoic acid (EPA) activates PPARγ signaling leading to cell cycle exit, lipid accumulation, and autophagy in human meibomian gland epithelial cells (hMGEC). Ocul Surf 2020; 18:427-437. [PMID: 32360782 DOI: 10.1016/j.jtos.2020.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/21/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of this study was to access the ability of the natural PPAR agonist, eicosapentaenoic acid (EPA), to activate PPAR gamma (γ) signaling leading to meibocyte differentiation in human meibomian gland epithelial cell (hMGEC). METHODS HMGEC were exposed to EPA, alone and in combination with the specific PPARγ antagonist, T0070907, to selectively block PPARγ signaling. Expression of PPARγ response genes were evaluated by qPCR. Effect on cell cycle was evaluated using Ki-67 labelling and western blots. During differentiation, autophagy was monitored using the Autophagy Tandem Sensor (ATS) and LysoTracker. Lipid accumulation was characterized by Stimulated Raman Scattering microscopy (SRS) and neutral lipid staining in combination with ER-Tracker, LysoTracker, and ATS. Autophagy was also investigated using western blotting. Seahorse XF analysis was performed to monitor mitochondrial function. RESULTS EPA specifically upregulated expression of genes related to lipid synthesis and induced cell cycle exit through reduced cyclin D1 expression and increased p21 and p27 expression. EPA also induced accumulation of lipid droplets in a time and dose dependent manner (P < 0.05) by specific PPARγ signaling. Lipid analysis identified both de novo synthesis and extracellular transport of lipid to form lipid droplets that were localized to the ER. PPARγ signaling also induced activation of AMPK-ULK1 signaling and autophagy, while inhibition of autophagy induced mitochondrial crisis with no effect on lipid accumulation. CONCLUSIONS EPA induces meibocyte differentiation through PPARγ activation that is characterized by cell cycle exit, de novo and transported lipid accumulation in the ER, and autophagy.
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109
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Kong C, Pilger C, Hachmeister H, Wei X, Cheung TH, Lai CSW, Lee NP, Tsia KK, Wong KKY, Huser T. High-contrast, fast chemical imaging by coherent Raman scattering using a self-synchronized two-colour fibre laser. LIGHT, SCIENCE & APPLICATIONS 2020; 9:25. [PMID: 32133128 PMCID: PMC7039946 DOI: 10.1038/s41377-020-0259-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 01/23/2020] [Accepted: 02/09/2020] [Indexed: 05/11/2023]
Abstract
Coherent Raman scattering (CRS) microscopy is widely recognized as a powerful tool for tackling biomedical problems based on its chemically specific label-free contrast, high spatial and spectral resolution, and high sensitivity. However, the clinical translation of CRS imaging technologies has long been hindered by traditional solid-state lasers with environmentally sensitive operations and large footprints. Ultrafast fibre lasers can potentially overcome these shortcomings but have not yet been fully exploited for CRS imaging, as previous implementations have suffered from high intensity noise, a narrow tuning range and low power, resulting in low image qualities and slow imaging speeds. Here, we present a novel high-power self-synchronized two-colour pulsed fibre laser that achieves excellent performance in terms of intensity stability (improved by 50 dB), timing jitter (24.3 fs), average power fluctuation (<0.5%), modulation depth (>20 dB) and pulse width variation (<1.8%) over an extended wavenumber range (2700-3550 cm-1). The versatility of the laser source enables, for the first time, high-contrast, fast CRS imaging without complicated noise reduction via balanced detection schemes. These capabilities are demonstrated in this work by imaging a wide range of species such as living human cells and mouse arterial tissues and performing multimodal nonlinear imaging of mouse tail, kidney and brain tissue sections by utilizing second-harmonic generation and two-photon excited fluorescence, which provides multiple optical contrast mechanisms simultaneously and maximizes the gathered information content for biological visualization and medical diagnosis. This work also establishes a general scenario for remodelling existing lasers into synchronized two-colour lasers and thus promotes a wider popularization and application of CRS imaging technologies.
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Affiliation(s)
- Cihang Kong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstr, 25, 33615 Bielefeld, Germany
| | - Christian Pilger
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstr, 25, 33615 Bielefeld, Germany
| | - Henning Hachmeister
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstr, 25, 33615 Bielefeld, Germany
| | - Xiaoming Wei
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
- Present Address: Division of Engineering and Applied Science, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125 USA
| | - Tom H. Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Cora S. W. Lai
- Department of Physiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Nikki P. Lee
- Department of Surgery, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kevin. K. Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Kenneth K. Y. Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstr, 25, 33615 Bielefeld, Germany
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110
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Liu X, Liu X, Rong P, Liu D. Recent advances in background-free Raman scattering for bioanalysis. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115765] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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111
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Shumyatsky P, Shi L, Sordillo LA, Budansky Y, Alfano RR. Comparison of continuous wave versus picosecond SRS and the resonance SRS effect. APPLIED OPTICS 2020; 59:622-627. [PMID: 32225186 DOI: 10.1364/ao.59.000622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/25/2019] [Indexed: 06/10/2023]
Abstract
Stimulated Raman scattering (SRS) is a powerful optical technique for probing the vibrational states of molecules in biological tissues and provides greater signal intensities than when using spontaneous Raman scattering. In this study, we examined the use of continuous wave (cw) and picosecond (ps) laser excitations to generate SRS signals in pure methanol, a carotene-methanol solution, acetone, and brain tissue samples. The cw-SRS system, which utilized two cw lasers, produced better signal-to-noise (S/N) than the conventional ps-SRS system, suggesting that the cw-SRS system is an efficient and cost-effective approach for studying SRS in complex systems like the brain. The cw-SRS approach will reduce the size of the SRS system, allowing for stimulated Raman gain/loss microscopy. In addition, we showed that there exists a resonance SRS (RSRS) effect from the carotene-methanol solution and brain tissue samples using cw laser excitations. The RSRS effect will further improve the signal-to-noise and may be utilized as an enhanced, label-free SRS microscopic tool for the study of biological tissues.
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112
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Wang Y, Xu J, Kong L, Liu T, Yi L, Wang H, Huang WE, Zheng C. Raman-deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota. Microb Biotechnol 2019; 13:572-583. [PMID: 31821744 PMCID: PMC7017835 DOI: 10.1111/1751-7915.13519] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022] Open
Abstract
Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of microorganisms at the single-cell level in gut microbial community. In this study, we applied Raman microspectroscopy and deuterium isotope probing (Raman-DIP) to quantitatively measure the metabolic activities of intestinal bacteria from two individuals and analysed lipids and phenylalanine metabolic pathways of functional microorganisms in situ. After anaerobically incubating the human faeces with heavy water (D2 O), D2 O with specific substrates (glucose, tyrosine, tryptophan and oleic acid) and deuterated glucose, the C-D band in single-cell Raman spectra appeared in some bacteria in faeces, due to the Raman shift from the C-H band. Such Raman shift was used to indicate the general metabolic activity and the activities in response to the specific substrates. In the two individuals' intestinal microbiota, the structures of the microbial communities were different and the general metabolic activities were 76 ± 1.0% and 30 ± 2.0%. We found that glucose, but not tyrosine, tryptophan and oleic acid, significantly stimulated metabolic activity of the intestinal bacteria. We also demonstrated that the bacteria within microbiota preferably used glucose to synthesize fatty acids in faeces environment, whilst they used glucose to synthesize phenylalanine in laboratory growth environment (e.g. LB medium). Our work provides a useful approach for investigating the metabolic activity in situ and revealing different pathways of human intestinal microbiota at the single-cell level.
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Affiliation(s)
- Yi Wang
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China.,Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.,Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Lingchao Kong
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Tang Liu
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingbo Yi
- Health Time Gene Institute, Shenzhen, 518000, China
| | | | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Chunmiao Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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113
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Ramanome technology platform for label-free screening and sorting of microbial cell factories at single-cell resolution. Biotechnol Adv 2019; 37:107388. [DOI: 10.1016/j.biotechadv.2019.04.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 01/09/2023]
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114
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Hill AH, Munger E, Francis AT, Manifold B, Fu D. Frequency Modulation Stimulated Raman Scattering Microscopy through Polarization Encoding. J Phys Chem B 2019; 123:8397-8404. [PMID: 31532680 DOI: 10.1021/acs.jpcb.9b07075] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Stimulated Raman scattering (SRS) microscopy is a powerful method for imaging molecular distributions based on their intrinsic vibrational contrast. However, despite a growing list of biological applications, SRS is frequently hindered by a parasitic background signal which both overpowers the signal in low-signal applications and makes the extraction of quantitative information from images challenging. Frequency modulation (FM) has been used to suppress this parasitic background. However, many FM-SRS methods require either the acquisition of multiple images or the addition of multiple optomechanical components and an extensive realignment procedure. Herein, we report a new procedure for alignment-free FM-SRS utilizing polarization encoding. We demonstrate the efficacy of this approach, along with parabolic amplification of the Stokes pulse, at removing parasitic background signals in SRS microscopy applications. We further highlight how this technique can be used to suppress Raman signals from major molecular species to unveil spectral signatures from nucleic acids in both murine brain tissue and whole blood. Due to its ease of use and demonstrated experimental capabilities, we expect this technique to see broad use in the SRS microscopy community.
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Affiliation(s)
- Andrew H Hill
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Eleanor Munger
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Andrew T Francis
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Bryce Manifold
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Dan Fu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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115
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Brinkmann M, Fast A, Hellwig T, Pence I, Evans CL, Fallnich C. Portable all-fiber dual-output widely tunable light source for coherent Raman imaging. BIOMEDICAL OPTICS EXPRESS 2019; 10:4437-4449. [PMID: 31565500 PMCID: PMC6757451 DOI: 10.1364/boe.10.004437] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/08/2019] [Indexed: 05/06/2023]
Abstract
We present a rapidly tunable dual-output all-fiber light source for coherent Raman imaging, based on a dispersively matched mode-locked laser pumping a parametric oscillator. Output pump and Stokes pulses with a maximal power of 170 and 400 mW, respectively, and equal durations of 7 ps could be generated. The tuning mechanism required no mechanical delay line, enabling all-electronic arbitrary wavelength switching across more than 2700 cm - 1 in less than 5 ms. The compact setup showed a reliable operation despite mechanical shocks of more than 25 m / s 2 and is, thus, well suited for operation in a mobile cart. Imaging mouse and human skin tissue with both the portable light source and a commercial laboratory-bound reference system yielded qualitatively equal results and verified the portable light source being well suited for coherent Raman microscopy.
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Affiliation(s)
- Maximilian Brinkmann
- Institute of Applied Physics, Corrensstr. 2, 48149 Münster, Germany
- Refined Laser Systems UG (haftungsbeschränkt), Münster, Germany
- Shared first author
| | - Alexander Fast
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Shared first author
| | - Tim Hellwig
- Institute of Applied Physics, Corrensstr. 2, 48149 Münster, Germany
- Refined Laser Systems UG (haftungsbeschränkt), Münster, Germany
| | - Isaac Pence
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Conor L Evans
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Carsten Fallnich
- Institute of Applied Physics, Corrensstr. 2, 48149 Münster, Germany
- Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Münster, Münster, Germany
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116
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Hu F, Shi L, Min W. Biological imaging of chemical bonds by stimulated Raman scattering microscopy. Nat Methods 2019; 16:830-842. [PMID: 31471618 DOI: 10.1038/s41592-019-0538-0] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/23/2019] [Indexed: 12/15/2022]
Abstract
All molecules consist of chemical bonds, and much can be learned from mapping the spatiotemporal dynamics of these bonds. Since its invention a decade ago, stimulated Raman scattering (SRS) microscopy has become a powerful modality for imaging chemical bonds with high sensitivity, resolution, speed and specificity. We introduce the fundamentals of SRS microscopy and review innovations in SRS microscopes and imaging probes. We highlight examples of exciting biological applications, and share our vision for potential future breakthroughs for this technology.
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Affiliation(s)
- Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA. .,Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
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117
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Frankel RD. Orthogonal beam ballistic backscatter stimulated Raman microscopy. OPTICS EXPRESS 2019; 27:22770-22786. [PMID: 31510563 DOI: 10.1364/oe.27.022770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
When the axial gain length of a stimulated Raman microscope is less than about 40% of the emission wavelength significant dipole-like ballistic backscatter will occur. Here we analyze a scanning microscope configured with orthogonal water dipping pump and probe objectives that satisfies this criterion. The pump beam focus may be a Gaussian spot or a droplet Bessel beam which minimizes the secondary Bessel beam lobes and provides multiple simultaneous pump focal spot regions. Radial and linearly polarized pump beams enable backscattered polarized signals along both transverse axes of the probe beam. Low level Mie backscatter is the primary photon noise source which should enable rapid sub-wavelength resolution 3-dimensional imaging of label-free Raman contrast for in-vivo pathology, as well as, imaging physiologic concentrations of Raman labelled metabolites and drugs.
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118
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Manifold B, Thomas E, Francis AT, Hill AH, Fu D. Denoising of stimulated Raman scattering microscopy images via deep learning. BIOMEDICAL OPTICS EXPRESS 2019; 10:3860-3874. [PMID: 31452980 PMCID: PMC6701518 DOI: 10.1364/boe.10.003860] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 05/06/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy is a label-free quantitative chemical imaging technique that has demonstrated great utility in biomedical imaging applications ranging from real-time stain-free histopathology to live animal imaging. However, similar to many other nonlinear optical imaging techniques, SRS images often suffer from low signal to noise ratio (SNR) due to absorption and scattering of light in tissue as well as the limitation in applicable power to minimize photodamage. We present the use of a deep learning algorithm to significantly improve the SNR of SRS images. Our algorithm is based on a U-Net convolutional neural network (CNN) and significantly outperforms existing denoising algorithms. More importantly, we demonstrate that the trained denoising algorithm is applicable to images acquired at different zoom, imaging power, imaging depth, and imaging geometries that are not included in the training. Our results identify deep learning as a powerful denoising tool for biomedical imaging at large, with potential towards in vivo applications, where imaging parameters are often variable and ground-truth images are not available to create a fully supervised learning training set.
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119
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Abstract
Cellular imaging is an active area of research that enables researchers to monitor cellular dynamics, as well as responses to various external stimuli (physiological stress, exogenous compounds, etc.). Stimulated Raman scattering (SRS) microscopy is one popular experimental tool used to image cells, largely because of its chemical specificity, high spatial resolution, and high image acquisition speed. In this Perspective, the theoretical background and experimental implementation of SRS microscopy are discussed and recent developments in the field of cellular imaging with SRS are highlighted and summarized.
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Affiliation(s)
- Andrew H Hill
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Dan Fu
- Department of Chemistry , University of Washington , Seattle , Washington 98195 , United States
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120
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Yang K, Li HZ, Zhu X, Su JQ, Ren B, Zhu YG, Cui L. Rapid Antibiotic Susceptibility Testing of Pathogenic Bacteria Using Heavy-Water-Labeled Single-Cell Raman Spectroscopy in Clinical Samples. Anal Chem 2019; 91:6296-6303. [PMID: 30942570 DOI: 10.1021/acs.analchem.9b01064] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Speeding up antibiotic susceptibility testing (AST) is urgently needed in clincial settings to guide fast and tailored antibiotic prescription before treatment. It remains a big challenge to achieve a sample-to-AST answer within a half working day directly from a clinical sample. Here we develop single-cell Raman spectroscopy coupled with heavy water labeling (Raman-D2O) as a rapid activity-based AST approach directly applicable for clinical urine samples. By rapidly transferring (15 min) bacteria in clinical urine for AST, the total assay time from receiving urine to binary susceptibility/resistance (S/R) readout was shortened to only 2.5 h. Moreover, by overcoming the nonsynchronous responses between microbial activity and microbial growth, together with setting a new S/R cutoff value based on relative C-D ratios, S/R of both pathogenic isolates and three clinical urines against antibiotics of different action mechanisms determined by Raman-D2O were all consistent with the slow standard AST assay used in clincial settings. This work promotes clinical practicability and faciliates antibiotic stewardship.
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Affiliation(s)
- Kai Yang
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Hong-Zhe Li
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , China.,University of Chinese Academy of Sciences , 19A Yuquan Road , Beijing 100049 , China
| | - Xuan Zhu
- The Second Affiliated Hospital of Xiamen Medical College , Xiamen 361021 , China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , China
| | - Bin Ren
- Department of Chemistry , Xiamen University , Xiamen 361005 , China
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , China.,State Key Laboratory of Urban and Regional Ecology , Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences , Beijing 100085 , China
| | - Li Cui
- Key Lab of Urban Environment and Health , Institute of Urban Environment, Chinese Academy of Sciences , Xiamen 361021 , China
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121
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Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A 2019; 116:6608-6617. [PMID: 30872474 DOI: 10.1073/pnas.1813044116] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Three-dimensional visualization of tissue structures using optical microscopy facilitates the understanding of biological functions. However, optical microscopy is limited in tissue penetration due to severe light scattering. Recently, a series of tissue-clearing techniques have emerged to allow significant depth-extension for fluorescence imaging. Inspired by these advances, we develop a volumetric chemical imaging technique that couples Raman-tailored tissue-clearing with stimulated Raman scattering (SRS) microscopy. Compared with the standard SRS, the clearing-enhanced SRS achieves greater than 10-times depth increase. Based on the extracted spatial distribution of proteins and lipids, our method reveals intricate 3D organizations of tumor spheroids, mouse brain tissues, and tumor xenografts. We further develop volumetric phasor analysis of multispectral SRS images for chemically specific clustering and segmentation in 3D. Moreover, going beyond the conventional label-free paradigm, we demonstrate metabolic volumetric chemical imaging, which allows us to simultaneously map out metabolic activities of protein and lipid synthesis in glioblastoma. Together, these results support volumetric chemical imaging as a valuable tool for elucidating comprehensive 3D structures, compositions, and functions in diverse biological contexts, complementing the prevailing volumetric fluorescence microscopy.
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122
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Pandey PC, Shukla S, Skoog SA, Boehm RD, Narayan RJ. Current Advancements in Transdermal Biosensing and Targeted Drug Delivery. SENSORS (BASEL, SWITZERLAND) 2019; 19:E1028. [PMID: 30823435 PMCID: PMC6427209 DOI: 10.3390/s19051028] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/19/2019] [Accepted: 02/21/2019] [Indexed: 01/10/2023]
Abstract
In this manuscript, recent advancements in the area of minimally-invasive transdermal biosensing and drug delivery are reviewed. The administration of therapeutic entities through the skin is complicated by the stratum corneum layer, which serves as a barrier to entry and retards bioavailability. A variety of strategies have been adopted for the enhancement of transdermal permeation for drug delivery and biosensing of various substances. Physical techniques such as iontophoresis, reverse iontophoresis, electroporation, and microneedles offer (a) electrical amplification for transdermal sensing of biomolecules and (b) transport of amphiphilic drug molecules to the targeted site in a minimally invasive manner. Iontophoretic delivery involves the application of low currents to the skin as well as the migration of polarized and neutral molecules across it. Transdermal biosensing via microneedles has emerged as a novel approach to replace hypodermic needles. In addition, microneedles have facilitated minimally invasive detection of analytes in body fluids. This review considers recent innovations in the structure and performance of transdermal systems.
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Affiliation(s)
- Prem C Pandey
- Department of Chemistry, Indian Institute of Technology (BHU), Varanasi 221005, India.
| | - Shubhangi Shukla
- Department of Chemistry, Indian Institute of Technology (BHU), Varanasi 221005, India.
| | - Shelby A Skoog
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Raleigh, NC 27695, USA.
| | - Ryan D Boehm
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Raleigh, NC 27695, USA.
| | - Roger J Narayan
- Joint Department of Biomedical Engineering, University of North Carolina and North Carolina State University, Raleigh, NC 27695, USA.
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123
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Phenazine production promotes antibiotic tolerance and metabolic heterogeneity in Pseudomonas aeruginosa biofilms. Nat Commun 2019; 10:762. [PMID: 30770834 PMCID: PMC6377615 DOI: 10.1038/s41467-019-08733-w] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022] Open
Abstract
Antibiotic efficacy can be antagonized by bioactive metabolites and other drugs present at infection sites. Pseudomonas aeruginosa, a common cause of biofilm-based infections, releases metabolites called phenazines that accept electrons to support cellular redox balancing. Here, we find that phenazines promote tolerance to clinically relevant antibiotics, such as ciprofloxacin, in P. aeruginosa biofilms and that this effect depends on the carbon source provided for growth. We couple stable isotope labeling with stimulated Raman scattering microscopy to visualize biofilm metabolic activity in situ. This approach shows that phenazines promote metabolism in microaerobic biofilm regions and influence metabolic responses to ciprofloxacin treatment. Consistent with roles of specific respiratory complexes in supporting phenazine utilization in biofilms, phenazine-dependent survival on ciprofloxacin is diminished in mutants lacking these enzymes. Our work introduces a technique for the chemical imaging of biosynthetic activity in biofilms and highlights complex interactions between bacterial products, their effects on biofilm metabolism, and the antibiotics we use to treat infections. Pseudomonas aeruginosa releases redox-active metabolites called phenazines. Here, the authors use metabolic imaging by stimulated Raman scattering microscopy to show that phenazines antagonize the effects of antibiotics on P. aeruginosa biofilms by modulating bacterial metabolism.
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124
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Deng S, Loterie D, Konstantinou G, Psaltis D, Moser C. Raman imaging through multimode sapphire fiber. OPTICS EXPRESS 2019; 27:1090-1098. [PMID: 30696180 DOI: 10.1364/oe.27.001090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We report on a sapphire fiber Raman imaging probe's use for challenging applications where access is severely restricted. Small-dimension Raman probes have been developed previously for various clinical applications because they show great capability for diagnosing disease states in bodily fluids, cells, and tissues. However, applications of these sub-millimeter diameter Raman probes were constrained by two factors: first, it is difficult to incorporate filters and focusing optics at such small scale; second, the weak Raman signal is often obscured by strong background noise from the fiber probe material, especially the most commonly used silica, which has a strong broad background noise in low wavenumbers (<500-1700 cm-1). Here, we demonstrate the thinnest-known imaging Raman probe with a 60 μm diameter Sapphire multimode fiber in which both excitation and signal collection pass through. This probe takes advantage of the low fluorescence and narrow Raman peaks of Sapphire, its inherent high temperature and corrosion resistance, and large numerical aperture (NA). Raman images of Polystyrene beads, carbon nanotubes, and CaSO4 agglomerations are obtained with a spatial resolution of 1 μm and a field of view of 30 μm. Our imaging results show that single polystyrene bead (~15 µm diameter) can be differentiated from a mixture with CaSO4 agglomerations, which has a close Raman shift.
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