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Omelchenko AN, Okotrub KA, Igonina TN, Rakhmanova TA, Okotrub SV, Rozhkova IN, Kozeneva VS, Amstislavsky SY, Surovtsev NV. Probing metabolism in mouse embryos using Raman spectroscopy and deuterium tags. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 325:125044. [PMID: 39236570 DOI: 10.1016/j.saa.2024.125044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 08/21/2024] [Accepted: 08/24/2024] [Indexed: 09/07/2024]
Abstract
The use of deuterated compounds is an interesting opportunity to expand the capabilities of Raman spectroscopy to study metabolism in living cells. Different biological objects have different tolerances to different deuterated compounds, and their metabolic chains may differ. Here, we explore the potential of this approach to probe metabolism in early mouse embryos. We investigated the Raman spectra of mouse embryos at different developmental stages cultured with deuterated amino acids, phenylalanine-d8 and leucine-d10, glucose-d7, and D2O. Embryos after in vitro culture with 20 % v/v D2O demonstrate Raman peak at 2186 cm-1 corresponding to newly synthesized proteins. Deuterated amino acids can slow down the development rate in 4-8 cell stage embryos, and deuterated glucose can be used at 2 mM concentration. For blastocyst, it was possible to achieve 75 % fraction of deuterated phenylalanine, when cultured with glucose, the maximal intensity ratio between CD and CH bands was 13.7 %. To demonstrate the capabilities of Raman spectroscopy reinforced by deuterium labeling, we investigated the short-term effect of cryopreservation and revealed that cryopreservation decreases the amount of saccharides in embryos and does not affect the activity of protein de novo synthesis.
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Affiliation(s)
- A N Omelchenko
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - K A Okotrub
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - T N Igonina
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - T A Rakhmanova
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia; Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - S V Okotrub
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - I N Rozhkova
- Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - V S Kozeneva
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia; Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - S Ya Amstislavsky
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia; Institute of Cytology and Genetics, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - N V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
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2
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Razi S, Tarcea N, Henkel T, Ravikumar R, Pistiki A, Wagenhaus A, Girnus S, Taubert M, Küsel K, Rösch P, Popp J. Raman-Activated, Interactive Sorting of Isotope-Labeled Bacteria. SENSORS (BASEL, SWITZERLAND) 2024; 24:4503. [PMID: 39065901 PMCID: PMC11281290 DOI: 10.3390/s24144503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024]
Abstract
Due to its high spatial resolution, Raman microspectroscopy allows for the analysis of single microbial cells. Since Raman spectroscopy analyzes the whole cell content, this method is phenotypic and can therefore be used to evaluate cellular changes. In particular, labeling with stable isotopes (SIPs) enables the versatile use and observation of different metabolic states in microbes. Nevertheless, static measurements can only analyze the present situation and do not allow for further downstream evaluations. Therefore, a combination of Raman analysis and cell sorting is necessary to provide the possibility for further research on selected bacteria in a sample. Here, a new microfluidic approach for Raman-activated continuous-flow sorting of bacteria using an optical setup for image-based particle sorting with synchronous acquisition and analysis of Raman spectra for making the sorting decision is demonstrated, showing that active cells can be successfully sorted by means of this microfluidic chip.
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Affiliation(s)
- Sepehr Razi
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
| | - Nicolae Tarcea
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Thomas Henkel
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
| | - Ramya Ravikumar
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Aikaterini Pistiki
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
| | - Annette Wagenhaus
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Sophie Girnus
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Martin Taubert
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Kirsten Küsel
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
| | - Jürgen Popp
- Leibniz-Institute of Photonic Technology, Member of the Leibniz Research Alliance—Leibniz Health Technologies, 07745 Jena, Germany; (S.R.); (N.T.); (T.H.); (A.P.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany; (M.T.); (K.K.)
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany; (R.R.); (P.R.)
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3
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Sun Y, Li S, Si Y, Niu Y, Yang J, Liu Y, Dong L, Zhu P, Dai J, Yang F. Dual-Stable-Isotope-Probed Raman microspectroscopy reveals the metabolic dynamic of Streptococcus mutans. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123318. [PMID: 37703791 DOI: 10.1016/j.saa.2023.123318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]
Abstract
Streptococcus mutans (S. mutans) is regarded as a cariogenic pathogen with the ability to metabolize sugars and form organic acids. However, its actual timely level of glucose consumption and cellular vitality in a polymicrobial culture system remains largely unknown. To tackle this challenge, we employed the S. mutans UA159 as a model and developed a dual-stable-isotope-probed Raman microspectroscopy method (Dual SIP-Raman) to simultaneously profile the general metabolic activity and glucose assimilative activity in situ. (i) Mono-SIP substrate feeding revealed that 0.5% 13C-glucose and 30% D2O were proper doses in the medium to obtain prominent and quantitative band shifts along with the 13C or D2O incorporation. In addition, the intensity of the 13C peak of phenylalanine (Phe) is proposed as a Raman-based biomarker for glucose utilization in a cell. (ii) The state of dual SIP substrate incorporation of 13C-glucose and D2O could be visualized by the corresponding spectral "red shifts" of Raman-scattered emissions; moreover, we also demonstrated that 13C/12C analysis was closely correlated with the C-D ratio. (iii) The application of the dual 13C-glucose and D2O feeding approach on a mock microbiota of S. mutans UA159 and C. albicans ATCC14053 revealed a stimulatory effect of fungus on both the glucose intake rate and general metabolic vitality of S. mutans UA159 (p < 0.05). Therefore, the 13C-glucose and D2O dual-feeding Raman Microspectroscopy approach is a valuable new tool for evaluating the glucose intake rate and general metabolic levels in situ, tracing the changing trend of the above metabolic activities, which is helpful to clarify the changes in the cariogenicity of oral microorganisms caused by the external environment at the single-cell level.
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Affiliation(s)
- Yanfei Sun
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Shanshan Li
- Changhai Hospital of Shanghai, Shanghai, 200433, China
| | - Yuan Si
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Yufen Niu
- School of Stomatology of Qingdao University, Qingdao 266003, China; Wuxi Stomatology Hospital, Jiangsu, Wuxi, 214000, China
| | - Jiazhen Yang
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Yuhan Liu
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Lei Dong
- School of Stomatology of Qingdao University, Qingdao 266003, China
| | - Pengfei Zhu
- Stomatological Hospital of Qingdao, Qingdao, 266000, China
| | - Jing Dai
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266003, China
| | - Fang Yang
- Qingdao Municipal Hospital, University of Health and Rehabilitation Sciences, Shandong, 26607, China; School of Stomatology of Qingdao University, Qingdao 266003, China.
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Omelchenko AN, Okotrub KA, Surovtsev NV. Raman spectroscopy of yeast cells cultured on a deuterated substrate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123262. [PMID: 37607454 DOI: 10.1016/j.saa.2023.123262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/13/2023] [Accepted: 08/13/2023] [Indexed: 08/24/2023]
Abstract
Raman spectroscopy of cells cultured in a deuterated substrate is a promising approach to the characterization of mass transfer and enzymatic reactions in living cells. Here, we studied the potential of this approach using the example of yeast cells cultured under aerobic and anaerobic conditions. In our experiments, unadapted to D2O Saccharomyces cerevisiae were cultured in a medium with different concentrations of deuterium oxide and deuterated glucose. It has been shown that the addition of even 10% heavy water leads to a general decrease in the amount of lipids in cells. In the Raman spectra of cells cultured at high concentrations of D2O, additional peaks are found, which are associated with the deuteration of entire chemical groups. We observed a similar effect in the ethanol synthesized by yeast fermentation, the deuteration of which also depends on the concentration of D2O. The results on the characterization of cell deuteration turned out to be in qualitative agreement with the known estimate that aerobic metabolism is 15 times more active than ethanol fermentation. The results of our work determine new limitations and prospects for further application and development of the Raman method of spectroscopy of deuterium tags.
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Affiliation(s)
- Anastasia N Omelchenko
- Novosibirsk State University, Novosibirsk, 630090, Russia; Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Konstantin A Okotrub
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Nikolay V Surovtsev
- Institute of Automation and Electrometry, Russian Academy of Sciences, Novosibirsk 630090, Russia
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Weng J, Müller K, Morgaienko O, Elsner M, Ivleva NP. Multi-element stable isotope Raman microspectroscopy of bacterial carotenoids unravels rare signal shift patterns and single-cell phenotypic heterogeneity. Analyst 2023; 148:128-136. [DOI: 10.1039/d2an01603f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Investigation of bacteria with D-carotenoids reveals unique Raman signatures, inclusive unexpected blue-shift. Simultaneous monitoring of 13C & D of carotenoids provides complementary information on cell growth and metabolic activity, respectively.
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Affiliation(s)
- Julian Weng
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Kara Müller
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Oleksii Morgaienko
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Martin Elsner
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Natalia P. Ivleva
- Technical University of Munich, Institute of Water Chemistry, Chair for Analytical Chemistry and Water Chemistry, Lichtenbergstr. 4, 85748 Garching, Germany
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6
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Jayan H, Sun DW, Pu H, Wei Q. Surface-enhanced Raman spectroscopy combined with stable isotope probing to assess the metabolic activity of Escherichia coli cells in chicken carcass wash water. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 280:121549. [PMID: 35792480 DOI: 10.1016/j.saa.2022.121549] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/31/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Rapid evaluation of the metabolic activity of microorganisms is crucial in the assessment of the disinfection ability of various antimicrobial agents in the food industry. In this study, surface-enhanced Raman spectroscopy combined with isotope probing was employed for the analysis of the disinfection of single bacterial cells in the chicken carcass wash water. The Raman signals from single Escherichia coli O157:H7 cells were enhanced by in situ synthesis of silver nanoparticles. The ΔCD of the cells grown in presence of 0.5% hydrogen peroxide and 50 ppm chlorine was 5.86 ± 1.86% and 5.1 ± 2.3%, respectively, which showed significant reduction compared with cells grown in the absence of disinfecting agents (19.86 ± 2.51%) after 2 h of incubation. The study proved that the proposed method had the potential to assess the metabolic activity of microorganisms in other food products and optimize the disinfection process.
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Affiliation(s)
- Heera Jayan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Qingyi Wei
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
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7
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Jayan H, Pu H, Sun DW. Analyzing macromolecular composition of E. Coli O157:H7 using Raman-stable isotope probing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 276:121217. [PMID: 35427921 DOI: 10.1016/j.saa.2022.121217] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Metabolic dynamics of bacterial cells is needed for understanding the correlation between changes in environmental conditions and cell metabolic activity. In this study, Raman spectroscopy combined with deuterium labelling was used to analyze the metabolic activity of a single Escherichia coli O157:H7 cell. The incorporation of deuterium from heavy water into cellular biomolecules resulted in the formation of carbon-deuterium (CD) peaks in the Raman spectra, indicating the cell metabolic activity. The broad vibrational peaks corresponding to CD and CH peaks encompassed different specific shifts of macromolecules such as protein, lipids, and nucleic acid. The utilization of tryptophan and oleic acid by the cell as the sole carbon source led to changes in cell lipid composition, as indicated by new peaks in the second derivative spectra. Thus, the proposed method could semi-quantitatively determine total metabolic activity, macromolecule specific identification, and lipid and protein metabolism in a single cell.
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Affiliation(s)
- Heera Jayan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Hongbin Pu
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China
| | - Da-Wen Sun
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; Academy of Contemporary Food Engineering, South China University of Technology, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Engineering and Technological Research Centre of Guangdong Province on Intelligent Sensing and Process Control of Cold Chain Foods, & Guangdong Province Engineering Laboratory for Intelligent Cold Chain Logistics Equipment for Agricultural Products, Guangzhou Higher Education Mega Centre, Guangzhou 510006, China; Food Refrigeration and Computerized Food Technology (FRCFT), Agriculture and Food Science Centre, University College Dublin, National University of Ireland, Belfield, Dublin 4, Ireland.
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Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME COMMUNICATIONS 2022; 2:52. [PMID: 37938730 PMCID: PMC9723565 DOI: 10.1038/s43705-022-00134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 05/08/2023]
Abstract
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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9
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Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
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10
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Azemtsop Matanfack G, Taubert M, Reilly-Schott V, Küsel K, Rösch P, Popp J. Phenotypic Differentiation of Autotrophic and Heterotrophic Bacterial Cells Using Raman-D 2O Labeling. Anal Chem 2022; 94:7759-7766. [PMID: 35608509 DOI: 10.1021/acs.analchem.1c04097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbon cycling is one of the major biogeochemical processes driven by bacteria. Autotrophic bacteria convert carbon dioxide (CO2) into organic compounds that are used by heterotrophs. Mixotrophic bacteria can employ both autotrophy and heterotrophy for growth. The characterization of the lifestyle of individual cells is essential to understand the microbial activity and thus reveal the implication of bacteria in the carbon flux. In this study, we used groundwater bacteria to investigate the potential of Raman-D2O labeling in combination with chemometrics to identify the carbon assimilation strategies of bacteria. Classification models were built using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Autotrophs assimilated a significantly higher amount (mean C-D ratio between 16.63 and 21.69%) of deuterium than heterotrophs. The C-D signal only provides information about the activity since it appears in the Raman-silent region, where no interference with the taxonomic information is expected. The classification between autotrophs and heterotrophs achieved an overall accuracy of 96.3%. In the validation step with an independent dataset containing species not included in the model, the PCA-LDA model achieved 100% accuracy. This demonstrated that the C-D signal contributed to the identification of autotrophic and heterotrophic bacterial cells. This work reports a robust, rapid, and nondestructive approach for the identification of single cells based on their carbon acquisition strategies. The present study foresees the potential of Raman-D2O labeling as a promising method for automated discrimination of in situ functional activities of bacteria in environmental systems.
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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., 07743 Jena, Germany
| | - Martin Taubert
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 07743 Jena, Germany
| | - Vincent Reilly-Schott
- Aquatic Geomicrobiology, Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Str. 159, 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, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 Jena, Germany.,Research Campus Infectognostics e.V., 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., 07743 Jena, Germany
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11
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No JH, Nishu SD, Hong JK, Lyou ES, Kim MS, Wee GN, Lee TK. Raman-Deuterium Isotope Probing and Metagenomics Reveal the Drought Tolerance of the Soil Microbiome and Its Promotion of Plant Growth. mSystems 2022; 7:e0124921. [PMID: 35103487 PMCID: PMC8805637 DOI: 10.1128/msystems.01249-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 01/07/2023] Open
Abstract
Drought has become a major agricultural threat leading crop yield loss. Although a few species of rhizobacteria have the ability to promote plant growth under drought, the drought tolerance of the soil microbiome and its relationship with the promotion of plant growth under drought are scarcely studied. This study aimed to develop a novel approach for assessing drought tolerance in agricultural land by quantitatively measuring microbial phenotypes using stable isotopes and Raman spectroscopy. Raman spectroscopy with deuterium isotope probing was used to identify the Raman signatures of drought effects from drought-tolerant bacteria. Counting drought-tolerant cells by applying these phenotypic properties to agricultural samples revealed that 0% to 52.2% of all measured single cells had drought-tolerant properties, depending on the soil sample. The proportions of drought-tolerant cells in each soil type showed similar tendencies to the numbers of revived pea plants cultivated under drought. The phenotype of the soil microbiome and plant behavior under drought conditions therefore appeared to be highly related. Studying metagenomics suggested that there was a reliable link between the phenotype and genotype of the soil microbiome that could explain mechanisms that promote plant growth in drought. In particular, the proportion of drought-tolerant cells was highly correlated with genes encoding phytohormone production, including tryptophan synthase and isopentenyl-diphosphate delta-isomerase; these enzymes are known to alleviate drought stress. Raman spectroscopy with deuterium isotope probing shows high potential as an alternative technology for quantitatively assessing drought tolerance through phenotypic analysis of the soil microbiome. IMPORTANCE Soil microbiome has played a critical role in the plant survival during drought. However, the drought tolerance of soil microbiome and its ability to promote plant growth under drought is still scarcely studied. In this study, we identified the Raman signature (i.e., phenotype) of drought effects from drought-tolerant bacteria in agricultural soil samples using Raman-deuterium isotope probing (Raman-DIP). Moreover, the number of drought-tolerant cells measured by Raman-DIP was highly related to the survival rate of plant cultivation under drought and the abundance of genes encoding phytohormone production alleviating drought stress in plant. These results suggest Raman-DIP is a promising technology for measuring drought tolerance of soil microbiome. This result give us important insight into further studies of a reliable link between phenotype and genotype of soil microbiome for future plant-bacteria interaction research.
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Affiliation(s)
- Jee Hyun No
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Susmita Das Nishu
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Jin-Kyung Hong
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Eun Sun Lyou
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Min Sung Kim
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Gui Nam Wee
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
| | - Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, Republic of Korea
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12
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Raman Stable Isotope Probing of Bacteria in Visible and Deep UV-Ranges. Life (Basel) 2021; 11:life11101003. [PMID: 34685375 PMCID: PMC8539138 DOI: 10.3390/life11101003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022] Open
Abstract
Raman stable isotope probing (Raman-SIP) is an excellent technique that can be used to access the overall metabolism of microorganisms. Recent studies have mainly used an excitation wavelength in the visible range to characterize isotopically labeled bacteria. In this work, we used UV resonance Raman spectroscopy (UVRR) to evaluate the spectral red-shifts caused by the uptake of isotopes (13C, 15N, 2H(D) and 18O) in E. coli cells. Moreover, we present a new approach based on the extraction of labeled DNA in combination with UVRR to identify metabolically active cells. The proof-of-principle study on E. coli revealed heterogeneities in the Raman features of both the bacterial cells and the extracted DNA after labeling with 13C, 15N, and D. The wavelength of choice for studying 18O- and deuterium-labeled cells is 532 nm is, while 13C-labeled cells can be investigated with visible and deep UV wavelengths. However, 15N-labeled cells are best studied at the excitation wavelength of 244 nm since nucleic acids are in resonance at this wavelength. These results highlight the potential of the presented approach to identify active bacterial cells. This work can serve as a basis for the development of new techniques for the rapid and efficient detection of active bacteria cells without the need for a cultivation step.
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13
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Azemtsop Matanfack G, Pistiki A, Rösch P, Popp J. Raman 18 O-labeling of bacteria in visible and deep UV-ranges. JOURNAL OF BIOPHOTONICS 2021; 14:e202100013. [PMID: 33773041 DOI: 10.1002/jbio.202100013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Raman stable isotope labeling with 2 H, 13 C or 15 N has been reported as an elegant approach to investigate cellular metabolic activity, which is of great importance to reveal the functions of microorganisms in native environments. A new strategy termed Raman 18 O-labeling was developed to probe the metabolic activity of bacteria. Raman 18 O-labeling refers to the combination of Raman microspectroscopy with 18 O-labeling using H218 O. At an excitation wavelength of 532 nm, the incorporation of 18 O into the amide I group of proteins and DNA/RNA bases was observed in Escherichia coli cells, while for an excitation wavelength electronically resonant with DNA or aromatic amino acid absorption at 244 nm 18 O assimilation was detected using chemometric tools rather than visual inspection. Raman 18 O-labeling at 532 nm combined with 2D correlation analysis confirmed the assimilation of 18 O in proteins and nucleic acids and revealed the growth strategy of E. coli cells; they underwent protein synthesis followed by nucleic acid synthesis. Independent cultural replicates at different incubation times corroborated the reproducibility of these results. The variations in spectral features of 18 O-labeled cells revealed changes in physiological information of cells. Hence, Raman 18 O-labeling could provide a powerful tool to identify metabolically active bacterial cells.
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Affiliation(s)
- Georgette Azemtsop Matanfack
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Aikaterini Pistiki
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology a member of the Leibniz Research Alliance Leibniz Health Technology (Leibniz-IPHT), Jena, Germany
- Research Campus Infectognostics e.v. Jena, Jena, Germany
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14
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Azemtsop Matanfack G, Taubert M, Guo S, Bocklitz T, Küsel K, Rösch P, Popp J. Monitoring Deuterium Uptake in Single Bacterial Cells via Two-Dimensional Raman Correlation Spectroscopy. Anal Chem 2021; 93:7714-7723. [PMID: 34014079 DOI: 10.1021/acs.analchem.1c01076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Raman-stable isotope labeling using heavy water (Raman-D2O) is attracting great interest as a fast technique with various applications ranging from the identification of pathogens in medical samples to the determination of microbial activity in the environment. Despite its widespread applications, little is known about the fundamental processes of hydrogen-deuterium (H/D) exchange, which are crucial for understanding molecular interactions in microorganisms. By combining two-dimensional (2D) correlation spectroscopy and Raman deuterium labeling, we have investigated H/D exchange in bacterial cells under time dependence. Most C-H stretching signals decreased in intensity over time, prior to the formation of the C-D stretching vibration signals. The intensity of the C-D signal gradually increased over time, and the shape of the C-D signal was more uniform after longer incubation times. Deuterium uptake showed high variability between the bacterial genera and mainly led to an observable labeling of methylene and methyl groups. Thus, the C-D signal encompassed a combination of symmetric and antisymmetric CD2 and CD3 stretching vibrations, depending on the bacterial genera. The present study allowed for the determination of the sequential order of deuterium incorporation into the functional groups of proteins, lipids, and nucleic acids and hence understanding the process of biomolecule synthesis and the growth strategies of different bacterial taxa. We present the combination of Raman-D2O labeling and 2D correlation spectroscopy as a promising approach to gain a fundamental understanding of molecular interactions in biological systems.
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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), Member of Leibniz Research Alliance "Health Technologies", 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), Member of Leibniz Research Alliance "Health Technologies", 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), Member of Leibniz Research Alliance "Health Technologies", 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, Puschstraße 4, 04103 Leipzig, Germany
| | - Petra Rösch
- Institute of Physical Chemistry and Abbe Center of Photonics (IPC), Friedrich-Schiller-University Jena, Helmholtzweg 4, 07743 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), Member of Leibniz Research Alliance "Health Technologies", Albert-Einstein-Straße 9, 07745 Jena, Germany.,Research Campus Infectognostics e.v. Jena, 07743 Jena, Germany
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15
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Chen M, Mo F, Meng H, Wang C, Guo J, Fu Y. Efficient Curing Sacrificial Agent-Induced Dual-Heterojunction Photoelectrochemical System for Highly Sensitive Immunoassay. Anal Chem 2021; 93:2464-2470. [DOI: 10.1021/acs.analchem.0c04485] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Min Chen
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Fangjing Mo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Hui Meng
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Cun Wang
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jiang Guo
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Yingzi Fu
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
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