1
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Huo B, Xia L, Hu Y, Li G. Flexible microfluidic co-recognition coupled with magnetic enrichment and silent SERS sensing for simultaneous analysis of bacteria in food. Biosens Bioelectron 2024; 255:116227. [PMID: 38552524 DOI: 10.1016/j.bios.2024.116227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/10/2024] [Accepted: 03/13/2024] [Indexed: 04/15/2024]
Abstract
Food safety represents a critical global public health issue, with safety challenges posed by foodborne pathogens garnering extensive attention. Therefore, we introduce a co-recognition, enrichment and sensing (CES) all-in-one strategy for analysis of bacteria with low background and high specificity. This method employs antimicrobial peptide (AMP) functionalized magnetic nanoparticles (MNPs) to enrich bacteria and uses aptamer@Au@PBA (KxMFe(CN)6 (M = Pb and Ni)) NPs as silent SERS tags. When both S. aureus and E. coli O157:H7 are present, the silent SERS probes could specifically label the target bacteria, forming a sandwich-like structure. This binding induces silent Raman shifts (2139 cm-1 and 2197 cm-1), enabling quantification of two bacteria. Coupling with the modular flexible microfluidics and magnetic control slider device, this platform facilitates rapid switching between magnetic loading and elution. The CES SERS method demonstrated linear relationships for both S. aureus and E. coli O157:H7 at 50-1600 cfu mL-1, with detection limits of 14 and 18 cfu mL-1, respectively. The method achieved recovery rates of 85.6-112% and relative standard deviations of 1.5-8.6%. Validation using the ELISA method revealed relative errors between -7.5 and 4.3%. The CES approach has potential applications in food safety, environmental monitoring, and biomedical diagnosis.
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Affiliation(s)
- Bingyang Huo
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ling Xia
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuling Hu
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510006, China
| | - Gongke Li
- School of Chemistry, Sun Yat-sen University, Guangzhou, 510006, China.
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2
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Vardaki MZ, Gregoriou VG, Chochos CL. Biomedical applications, perspectives and tag design concepts in the cell - silent Raman window. RSC Chem Biol 2024; 5:273-292. [PMID: 38576725 PMCID: PMC10989507 DOI: 10.1039/d3cb00217a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/12/2024] [Indexed: 04/06/2024] Open
Abstract
Spectroscopic studies increasingly employ Raman tags exhibiting a signal in the cell - silent region of the Raman spectrum (1800-2800 cm-1), where bands arising from biological molecules are inherently absent. Raman tags bearing functional groups which contain a triple bond, such as alkyne and nitrile or a carbon-deuterium bond, have a distinct vibrational frequency in this region. Due to the lack of spectral background and cell-associated bands in the specific area, the implementation of those tags can help overcome the inherently poor signal-to-noise ratio and presence of overlapping Raman bands in measurements of biological samples. The cell - silent Raman tags allow for bioorthogonal imaging of biomolecules with improved chemical contrast and they have found application in analyte detection and monitoring, biomarker profiling and live cell imaging. This review focuses on the potential of the cell - silent Raman region, reporting on the tags employed for biomedical applications using variants of Raman spectroscopy.
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Affiliation(s)
- Martha Z Vardaki
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
| | - Vasilis G Gregoriou
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
| | - Christos L Chochos
- Institute of Chemical Biology, National Hellenic Research Foundation, 48 Vassileos Constantinou Avenue Athens 11635 Greece
- Advent Technologies SA, Stadiou Street, Platani Rio Patras 26504 Greece
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3
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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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4
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Moriyama S, Mae M, Shibata D, Yamakoshi H, Kajimoto S, Nakabayashi T, Ishimoto T, Mogi K, Sajiki H, Akai S, Sawama Y. Multiple deuteration of triphenylphosphine and live-cell Raman imaging of deuterium-incorporated Mito-Q. Chem Commun (Camb) 2023; 59:12100-12103. [PMID: 37721453 DOI: 10.1039/d3cc04410f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
All aromatic C-H bonds of triphenylphosphine (PPh3) were efficiently replaced by C-D bonds using Ru/C and Ir/C co-catalysts in 2-PrOH and D2O, an inexpensive deuterium source. Furthermore, non-radioactive and safe deuterium-incorporated Mito-Q (drug candidate) was prepared from deuterated PPh3 and used for the live-cell Raman imaging to evaluate the mitochondrial uptake.
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Affiliation(s)
- Shogo Moriyama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Miyu Mae
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Daiki Shibata
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Yamakoshi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Shinji Kajimoto
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
- JST PRESTO, 4-1-8 Hon-cho, Kawaguchi, Saitama 332-0012, Japan
| | - Takakazu Nakabayashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takayoshi Ishimoto
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-4-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8527, Japan
| | - Kaiki Mogi
- Gifu Pharmaceutical University, 1-25-4-Daigaku-nishi, Gifu 501-1196, Japan
| | - Hironao Sajiki
- Gifu Pharmaceutical University, 1-25-4-Daigaku-nishi, Gifu 501-1196, Japan
| | - Shuji Akai
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
| | - Yoshinari Sawama
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6, Yamada-oka, Suita, Osaka 565-0871, Japan.
- Deuterium Science Research Unit, Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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5
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Liao HX, Bando K, Li M, Fujita K. Multifocal Raman Spectrophotometer for Examining Drug-Induced and Chemical-Induced Cellular Changes in 3D Cell Spheroids. Anal Chem 2023; 95:14616-14623. [PMID: 37725051 DOI: 10.1021/acs.analchem.3c02129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Cell spheroids offer alternative in vitro cell models to monolayer cultured cells because they express complexities similar to those of in vivo tissues, such as cellular responses to drugs and chemicals. Raman spectroscopy emerged as a powerful analytical tool for detecting chemical changes in living cells because it nondestructively provides vibrational information regarding a target. Although multiple iterations are required in drug screening to determine drugs to treat cell spheroids and assess the inter-spheroid heterogeneity, current Raman applications used in spheroids analysis allow the observation of only a few spheroids owing to the low throughput of Raman spectroscopy. In this study, we developed a multifocal Raman spectrophotometer that enables simultaneous analysis of multiple spheroids in separate wells of a regular 96-well plate. By utilizing 96 focal spots excitation and parallel signal collection, our system can improve the throughput by approximately 2 orders of magnitude compared to a conventional single-focus Raman microscope. The Raman spectra of HeLa cell spheroids treated with anticancer drugs and HepG2 cell spheroids treated with free fatty acids were measured simultaneously, and concentration-dependent cellular responses were observed in both studies. Using the multifocal Raman spectrophotometer, we rapidly observed chemical changes in spheroids, and thus, this system can facilitate the application of Raman spectroscopy in analyzing the cellular responses of spheroids.
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Affiliation(s)
- Hao-Xiang Liao
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuki Bando
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- AIST Advanced Photonics and Biosensing Open Innovation Laboratory, Suita, Osaka 565-0871, Japan
| | - Menglu Li
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- AIST Advanced Photonics and Biosensing Open Innovation Laboratory, Suita, Osaka 565-0871, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- AIST Advanced Photonics and Biosensing Open Innovation Laboratory, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Suita, Osaka 565-0871, Japan
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6
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Spratt SJ, Mizuguchi T, Akaboshi H, Kosakamoto H, Okada R, Obata F, Ozeki Y. Imaging the uptake of deuterated methionine in Drosophila with stimulated Raman scattering. Front Chem 2023; 11:1141920. [PMID: 37065821 PMCID: PMC10090404 DOI: 10.3389/fchem.2023.1141920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
Introduction: Visualizing small individual biomolecules at subcellular resolution in live cells and tissues can provide valuable insights into metabolic activity in heterogeneous cells, but is challenging.Methods: Here, we used stimulated Raman scattering (SRS) microscopy to image deuterated methionine (d-Met) incorporated into Drosophila tissues in vivo.Results: Our results demonstrate that SRS can detect a range of previously uncharacterized cell-to-cell differences in d-Met distribution within a tissue at the subcellular level.Discussion: These results demonstrate the potential of SRS microscopy for metabolic imaging of less abundant but important amino acids such as methionine in tissue.
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Affiliation(s)
- Spencer J. Spratt
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takaha Mizuguchi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hikaru Akaboshi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yasuyuki Ozeki,
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7
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Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases. Int J Mol Sci 2023; 24:ijms24032384. [PMID: 36768712 PMCID: PMC9917237 DOI: 10.3390/ijms24032384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.
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8
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Hyperglycemia and cancer in human lung carcinoma by means of Raman spectroscopy and imaging. Sci Rep 2022; 12:18561. [PMID: 36329066 PMCID: PMC9633797 DOI: 10.1038/s41598-022-21483-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Raman spectroscopy and Raman imaging were used to identify the biochemical and structural features of human cancer lung cells (CCL-185) and the cancer cells supplemented with glucose and deuterated glucose at normal and hyperglycemia conditions. We found that isotope substitution of glucose by deuterated glucose allows to separate de novo lipid synthesis from exogenous uptake of lipids obtained from the diet. We demonstrated that glucose is largely utilized for de novo lipid synthesis. Our results provide a direct evidence that high level of glucose decreases the metabolism via oxidative phosphorylation in mitochondria in cancer cells and shifts the metabolism to glycolysis via Warburg effect. It suggests that hyperglycemia is a factor that may contribute to a more malignant phenotype of cancer cells by inhibition of oxidative phosphorylation and apoptosis.
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9
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Dodo K, Fujita K, Sodeoka M. Raman Spectroscopy for Chemical Biology Research. J Am Chem Soc 2022; 144:19651-19667. [PMID: 36216344 PMCID: PMC9635364 DOI: 10.1021/jacs.2c05359] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Indexed: 11/29/2022]
Abstract
In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.
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Affiliation(s)
- Kosuke Dodo
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumasa Fujita
- Department
of Applied Physics, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Institute
for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
- AIST-Osaka
University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science
and Technology (AIST), Suita, Osaka 565-0871, Japan
| | - Mikiko Sodeoka
- Synthetic
Organic Chemistry Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Catalysis
and Integrated Research Group, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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10
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Qi Z, Liu C. Metabolic characteristics and markers in viable but nonculturable state of Pseudomonas aeruginosa induced by chlorine stress. ENVIRONMENTAL RESEARCH 2022; 214:114111. [PMID: 35987374 DOI: 10.1016/j.envres.2022.114111] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Many Gram-negative pathogens enter the viable but nonculturable (VBNC) state to resist external environmental stress (such as disinfection). However, little is known about the metabolic properties, especially for the metabolic markers, of VBNC bacteria, which impedes the development of efficient disinfection technologies and causes more potential health risks. In this study, we analyzed the metabolic characteristics of chlorine stress-induced VBNC Pseudomonas aeruginosa at the population and single-cell levels. The overall metabolic activity of VBNC bacteria showed a downward trend, but the glyoxylate cycle, fatty acid and glycerophospholipid metabolism pathways were up-regulated. Based on the metabolic profiles of VBNC bacteria, nine metabolic markers (pyruvate, glyoxylate, guanine, glutamate, sn glycero-3-phos-phocholine, fatty acid, D-alanine, glutathione, N-Butanoyl-D-homoserine lactone) were determined. The results of single-cell Raman spectroscopy showed that the metabolic activity of VBNC bacteria was significantly reduced, but showed more significant metabolic heterogeneity. The redshift of the Raman peaks of 15N and 13C labeled VBNC bacteria was significantly weaker than that of the culturable bacteria, suggesting that the VBNC bacteria have a reduced ability to synthesize proteins, nucleotides, phospholipids, and carbohydrates. The result of this study can help to better understand the metabolic mechanisms and energy management strategy of VBNC bacteria, to achieve precise identification and effective control of VBNC bacteria.
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Affiliation(s)
- Zheng Qi
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China
| | - Chunguang Liu
- School of Environmental Science and Engineering, Shandong Key Laboratory of Environmental Processes and Health, China-America CRC for Environment & Health of Shandong Province, Shandong University, 72# Jimo Binhai Road, Qingdao, Shandong, 266237, PR China; Guangdong Provincial Key Laboratory of Environmental Protection and Resources Utilization, Guangdong Province, PR China.
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11
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Deuterium Raman imaging for lipid analysis. Curr Opin Chem Biol 2022; 70:102181. [DOI: 10.1016/j.cbpa.2022.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/28/2022] [Accepted: 05/31/2022] [Indexed: 11/18/2022]
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12
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Cui D, Kong L, Wang Y, Zhu Y, Zhang C. In situ identification of environmental microorganisms with Raman spectroscopy. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 11:100187. [PMID: 36158754 PMCID: PMC9488013 DOI: 10.1016/j.ese.2022.100187] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 05/28/2023]
Abstract
Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.
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Affiliation(s)
- Dongyu Cui
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yi Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, University of Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
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13
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Li Y, Zhang W, Fung AA, Shi L. DO-SRS imaging of diet regulated metabolic activities in Drosophila during aging processes. Aging Cell 2022; 21:e13586. [PMID: 35257470 PMCID: PMC9009230 DOI: 10.1111/acel.13586] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 12/27/2022] Open
Abstract
Lipid metabolism plays crucial roles during aging processes, but how it is regulated by diets and how it interplays with aging still remain unclear. We proposed a new optical imaging platform by integrating heavy water (D2 O) probing with stimulated Raman scattering (DO-SRS) microscopy, for the first time, to directly visualize and quantify lipid metabolism regulated by different diets and insulin signaling pathway in Drosophila fat body during aging. We found that calorie restriction, low protein diet, and (moderately) high protein and high sucrose diets enhanced lipid turnover in flies at all ages, while (moderately) high fructose and glucose diets only promoted lipid turnover in aged flies. The measured lipid turnover enhancements under diverse diets were due to different mechanisms. High protein diet shortened the lifespan while all other diets extended the lifespan. Downregulating the insulin signaling pathway enhanced lipid turnover, which is likely related to lifespan increase, while upregulating insulin signaling pathway decreased lipid turnover that would shorten the lifespan. Our study offers the first approach to directly visualize spatiotemporal alterations of lipid turnover in aging Drosophila in situ, for a better understanding of the interconnections between lipid metabolism, diets, and aging.
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Affiliation(s)
- Yajuan Li
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Wenxu Zhang
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anthony A. Fung
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Lingyan Shi
- Department of BioengineeringUniversity of California San DiegoLa JollaCaliforniaUSA
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14
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Yonamine Y, Asai T, Suzuki Y, Ito T, Ozeki Y, Hoshino Y. Probing the Biogenesis of Polysaccharide Granules in Algal Cells at Sub-Organellar Resolution via Raman Microscopy with Stable Isotope Labeling. Anal Chem 2021; 93:16796-16803. [PMID: 34870976 DOI: 10.1021/acs.analchem.1c03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Phototrophs assimilate CO2 into organic compounds that accumulate in storage organelles. Elucidation of the carbon dynamics of storage organelles could enhance the production efficiency of valuable compounds and facilitate the screening of strains with high photosynthetic activity. To comprehensively elucidate the carbon dynamics of these organelles, the intraorganellar distribution of the carbon atoms that accumulate at specific time periods should be probed. In this study, the biosynthesis of polysaccharides in storage organelles was spatiotemporally probed via stimulated Raman scattering (SRS) microscopy using a stable isotope (13C) as the tracking probe. Paramylon granules (a storage organelle of β-1,3-glucan) accumulated in a unicellular photosynthetic alga, Euglena gracilis, were investigated as a model organelle. The carbon source of the culture medium was switched from NaH12CO3 to NaH13CO3 during the production of the paramylon granules; this resulted in the distribution of the 12C and 13C constituents in the granules, so that the biosynthetic process could be tracked. Taking advantage of high-resolution SRS imaging and label switching, the localization of the 12C and 13C constituents inside a single paramylon granule could be visualized in three dimensions, thus revealing the growth process of paramylon granules. We propose that this method can be used for comprehensive elucidation of the dynamic activities of storage organelles.
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Affiliation(s)
- Yusuke Yonamine
- Research Institute for Electronic Science, Hokkaido University, Kita21, Nishi10, Kita-ku, Sapporo 001-0021, Japan
| | - Takuya Asai
- Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yuta Suzuki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takuro Ito
- Department of Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Japan Science and Technology Agency, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan.,Department of Creative Engineering, National Institute of Technology (KOSEN), Tsuruoka College, 104 Sawada, Inooka, Tsuruoka, Yamagata 997-8511, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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15
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Bagheri P, Hoang K, Fung AA, Hussain S, Shi L. Visualizing Cancer Cell Metabolic Dynamics Regulated With Aromatic Amino Acids Using DO-SRS and 2PEF Microscopy. Front Mol Biosci 2021; 8:779702. [PMID: 34977157 PMCID: PMC8714916 DOI: 10.3389/fmolb.2021.779702] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/22/2021] [Indexed: 12/19/2022] Open
Abstract
Oxidative imbalance plays an essential role in the progression of many diseases that include cancer and neurodegenerative diseases. Aromatic amino acids (AAA) such as phenylalanine and tryptophan have the capability of escalating oxidative stress because of their involvement in the production of Reactive Oxygen Species (ROS). Here, we use D2O (heavy water) probed stimulated Raman scattering microscopy (DO-SRS) and two Photon Excitation Fluorescence (2PEF) microscopy as a multimodal imaging approach to visualize metabolic changes in HeLa cells under excess AAA such as phenylalanine or trytophan in culture media. The cellular spatial distribution of de novo lipogenesis, new protein synthesis, NADH, Flavin, unsaturated lipids, and saturated lipids were all imaged and quantified in this experiment. Our studies reveal ∼10% increase in de novo lipogenesis and the ratio of NADH to flavin, and ∼50% increase of the ratio of unsaturated lipids to saturated lipid in cells treated with excess phenylalanine or trytophan. In contrast, these cells exhibited a decrease in the protein synthesis rate by ∼10% under these AAA treatments. The cellular metabolic activities of these biomolecules are indicators of elevated oxidative stress and mitochondrial dysfunction. Furthermore, 3D reconstruction images of lipid droplets were acquired and quantified to observe their spatial distribution around cells’ nuceli under different AAA culture media. We observed a higher number of lipid droplets in excess AAA conditions. Our study showcases that DO-SRS imaging can be used to quantitatively study how excess AAA regulates metabolic activities of cells with subcellular resolution in situ.
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16
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Abstract
Emerging studies have shown that lipid metabolism plays an important role in aging. High resolution in situ imaging of lipid metabolic dynamics inside cells and tissues affords a novel and potent approach for understanding many biological processes such as aging. Here we established a new optical imaging platform that combines D2O-probed stimulated Raman scattering (DO-SRS) imaging microscopy and a Drosophila model to directly visualize metabolic activities in situ during aging. The sub-cellular spatial distribution of de novo lipogenesis in the fat body was quantitatively imaged and examined. We discovered a dramatic decrease in lipid turnover in 35-day-old flies. Decreases in protein turnover occurred earlier than lipids (25-day vs. 35-day), and there are many proteins localized on the cell and lipid droplet membrane. This suggests that protein metabolism may act as a prerequisite for lipid metabolism during aging. This alteration of maintenance of protein turnover indicates disrupted lipid metabolism. We further found a significantly higher lipid turnover rate in large LDs, indicating more active metabolism in large LDs, suggesting that large and small LDs play different roles in metabolism to maintain cellular homeostasis. This is the first study that directly visualizes spatiotemporal alterations of lipid (and protein) metabolism in Drosophila during the aging process. Our study not only demonstrates a new imaging platform for studying lipid metabolism, but also unravels the important interconnections between lipid metabolism and aging.
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Affiliation(s)
- Yajuan Li
- Department of Bioengineering, University of California San Diego, USA.
| | - Wenxu Zhang
- Department of Bioengineering, University of California San Diego, USA.
| | - Anthony A Fung
- Department of Bioengineering, University of California San Diego, USA.
| | - Lingyan Shi
- Department of Bioengineering, University of California San Diego, USA.
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17
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Chirizzi C, Morasso C, Caldarone AA, Tommasini M, Corsi F, Chaabane L, Vanna R, Bombelli FB, Metrangolo P. A Bioorthogonal Probe for Multiscale Imaging by 19F-MRI and Raman Microscopy: From Whole Body to Single Cells. J Am Chem Soc 2021; 143:12253-12260. [PMID: 34320323 PMCID: PMC8397317 DOI: 10.1021/jacs.1c05250] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Molecular imaging
techniques are essential tools for better investigating
biological processes and detecting disease biomarkers with improvement
of both diagnosis and therapy monitoring. Often, a single imaging
technique is not sufficient to obtain comprehensive information at
different levels. Multimodal diagnostic probes are key tools to enable
imaging across multiple scales. The direct registration of in vivo imaging markers with ex vivo imaging
at the cellular level with a single probe is still challenging. Fluorinated
(19F) probes have been increasingly showing promising potentialities
for in vivo cell tracking by 19F-MRI.
Here we present the unique features of a bioorthogonal 19F-probe that enables direct signal correlation of MRI with Raman
imaging. In particular, we reveal the ability of PERFECTA, a superfluorinated
molecule, to exhibit a remarkable intense Raman signal distinct from
cell and tissue fingerprints. Therefore, PERFECTA combines in a single
molecule excellent characteristics for both macroscopic in
vivo19F-MRI, across the whole body, and microscopic
imaging at tissue and cellular levels by Raman imaging.
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Affiliation(s)
- Cristina Chirizzi
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Carlo Morasso
- Istituti Clinici Scientifici Maugeri IRCCS, Via S. Maugeri 4, 27100 Pavia, Italy
| | | | - Matteo Tommasini
- Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Fabio Corsi
- Istituti Clinici Scientifici Maugeri IRCCS, Via S. Maugeri 4, 27100 Pavia, Italy.,Department of Biomedical and Clinical Sciences "Luigi Sacco", Università di Milano, Via G. B. Grassi 74, 20157 Milan, Italy
| | - Linda Chaabane
- Experimental Neurology (INSPE) and Experimental Imaging Center (CIS), Neuroscience Division, IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy
| | - Renzo Vanna
- CNR-Institute for Photonics and Nanotechnologies (IFN-CNR), Department of Physics, Politecnico di Milano, Piazza Leonardo Da Vinci 32, 20133 Milan, Italy
| | - Francesca Baldelli Bombelli
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
| | - Pierangelo Metrangolo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials, and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via Luigi Mancinelli 7, 20131 Milan, Italy
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18
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Aguilar-Toalá JE, Hall FG, Urbizo-Reyes UC, Garcia HS, Vallejo-Cordoba B, González-Córdova AF, Hernández-Mendoza A, Liceaga AM. In Silico Prediction and In Vitro Assessment of Multifunctional Properties of Postbiotics Obtained From Two Probiotic Bacteria. Probiotics Antimicrob Proteins 2021; 12:608-622. [PMID: 31280464 DOI: 10.1007/s12602-019-09568-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, a global metabolite profile using Raman spectroscopy analysis was obtained in order to predict, by an in silico prediction of activity spectra for substance approach, the bioactivities of the intracellular content (IC) and cell wall (CW) fractions obtained from Lactobacillus casei CRL 431 and Bacillus coagulans GBI-30 strains. Additionally, multifunctional in vitro bioactivity of IC and CW fractions was also assessed. The metabolite profile revealed a variety of compounds (fatty acids, amino acids, coenzyme, protein, amino sugars), with significant probable activities (Pa > 0.7) as immune-stimulant, anti-inflammatory, neuroprotective, antiproliferative, immunomodulator, and antineoplastic, among others. Moreover, in vitro assays exhibited that both IC and CW fractions presented angiotensin-converting enzyme-inhibitory (> 90%), chelating (> 79%), and antioxidant (ca. 22-57 cellular antioxidant activity units) activities. Our findings based on in silico and in vitro analyses suggest that L. casei CRL 431 and B. coagulans GBI-30 strains appear to be promising sources of postbiotics and may impart health benefits by their multifunctional properties.
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Affiliation(s)
- J E Aguilar-Toalá
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km. 0.6, 83304, Hermosillo, Sonora, Mexico.,Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN, 47907, USA
| | - F G Hall
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN, 47907, USA
| | - U C Urbizo-Reyes
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN, 47907, USA
| | - H S Garcia
- UNIDA Tecnológico Nacional de México, Instituto Tecnológico de Veracruz, M.A. de Quevedo 2279, Col. Formando Hogar, 91897, Veracruz, Veracruz, Mexico
| | - B Vallejo-Cordoba
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km. 0.6, 83304, Hermosillo, Sonora, Mexico
| | - A F González-Córdova
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km. 0.6, 83304, Hermosillo, Sonora, Mexico
| | - A Hernández-Mendoza
- Laboratorio de Química y Biotecnología de Productos Lácteos, Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Carretera a La Victoria km. 0.6, 83304, Hermosillo, Sonora, Mexico.
| | - A M Liceaga
- Department of Food Science, Purdue University, 745 Agriculture Mall Dr, West Lafayette, IN, 47907, USA.
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19
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Dodo K, Sato A, Tamura Y, Egoshi S, Fujiwara K, Oonuma K, Nakao S, Terayama N, Sodeoka M. Synthesis of deuterated γ-linolenic acid and application for biological studies: metabolic tuning and Raman imaging. Chem Commun (Camb) 2021; 57:2180-2183. [PMID: 33527102 DOI: 10.1039/d0cc07824g] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
γ-Linolenic acid (GLA) is reported to show tumor-selective cytotoxicity through unidentified mechanisms. Here, to assess the involvement of oxidized metabolites of GLA, we synthesized several deuterated GLAs and evaluated their metabolism and cytotoxicity towards normal human fibroblast WI-38 cells and VA-13 tumor cells generated from WI-38 by transformation with SV40 virus. Deuteration of GLA suppressed both metabolism and cytotoxicity towards WI-38 cells and increased the selectivity for VA-13 cells. Fully deuterated GLA was visualized by Raman imaging, which indicated that GLA is accumulated in intracellular lipid droplets of VA-13 cells. Our results suggest the tumor-selective cytotoxicity is due to GLA itself, not its oxidized metabolites.
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Affiliation(s)
- Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and Sodeoka Live Cell Chemistry Project, ERATO, Japan Sciences and Technology Agency, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ayato Sato
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and Sodeoka Live Cell Chemistry Project, ERATO, Japan Sciences and Technology Agency, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuki Tamura
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and Sodeoka Live Cell Chemistry Project, ERATO, Japan Sciences and Technology Agency, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Syusuke Egoshi
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Koichi Fujiwara
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kana Oonuma
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shuhei Nakao
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Naoki Terayama
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan. and Sodeoka Live Cell Chemistry Project, ERATO, Japan Sciences and Technology Agency, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and AMED-CREST, Japan Agency for Medical Research and Development, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Xu J, Yu T, Zois CE, Cheng JX, Tang Y, Harris AL, Huang WE. Unveiling Cancer Metabolism through Spontaneous and Coherent Raman Spectroscopy and Stable Isotope Probing. Cancers (Basel) 2021; 13:1718. [PMID: 33916413 PMCID: PMC8038603 DOI: 10.3390/cancers13071718] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/24/2021] [Accepted: 03/28/2021] [Indexed: 11/25/2022] Open
Abstract
Metabolic reprogramming is a common hallmark in cancer. The high complexity and heterogeneity in cancer render it challenging for scientists to study cancer metabolism. Despite the recent advances in single-cell metabolomics based on mass spectrometry, the analysis of metabolites is still a destructive process, thus limiting in vivo investigations. Being label-free and nonperturbative, Raman spectroscopy offers intrinsic information for elucidating active biochemical processes at subcellular level. This review summarizes recent applications of Raman-based techniques, including spontaneous Raman spectroscopy and imaging, coherent Raman imaging, and Raman-stable isotope probing, in contribution to the molecular understanding of the complex biological processes in the disease. In addition, this review discusses possible future directions of Raman-based technologies in cancer research.
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Affiliation(s)
- Jiabao Xu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
| | - Tong Yu
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
| | - Christos E. Zois
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, UK;
- Department of Radiotherapy and Oncology, School of Health, Democritus University of Thrace, 68100 Alexandroupolis, Greece
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MS 02215, USA;
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China;
| | - Adrian L. Harris
- Molecular Oncology Laboratories, Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DS, UK;
| | - Wei E. Huang
- Department of Engineering Science, University of Oxford, Oxford OX1 3PJ, UK;
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21
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:7715-7720. [PMID: 38505234 PMCID: PMC10946860 DOI: 10.1002/ange.202016802] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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22
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. Angew Chem Int Ed Engl 2021; 60:7637-7642. [PMID: 33491852 PMCID: PMC8048481 DOI: 10.1002/anie.202016802] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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23
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Fleissner F, Kumar S, Klein N, Wirth D, Dhiman R, Schneider D, Bonn M, Parekh SH. Tension Causes Unfolding of Intracellular Vimentin Intermediate Filaments. ACTA ACUST UNITED AC 2020; 4:e2000111. [DOI: 10.1002/adbi.202000111] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/18/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Frederik Fleissner
- Department of Molecular Spectroscopy Max Planck Institute for Polymer Research Mainz 55128 Germany
| | - Sachin Kumar
- Department of Molecular Spectroscopy Max Planck Institute for Polymer Research Mainz 55128 Germany
- Department of Biomedical Engineering University of Texas at Austin Austin TX 78712 USA
| | - Noreen Klein
- Institute of Pharmacy and Biochemistry Johannes Gutenberg‐University Mainz 55128 Germany
| | - Daniel Wirth
- Institute of Pharmacy and Biochemistry Johannes Gutenberg‐University Mainz 55128 Germany
| | - Ravi Dhiman
- Department of Molecular Spectroscopy Max Planck Institute for Polymer Research Mainz 55128 Germany
| | - Dirk Schneider
- Institute of Pharmacy and Biochemistry Johannes Gutenberg‐University Mainz 55128 Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy Max Planck Institute for Polymer Research Mainz 55128 Germany
| | - Sapun H. Parekh
- Department of Molecular Spectroscopy Max Planck Institute for Polymer Research Mainz 55128 Germany
- Department of Biomedical Engineering University of Texas at Austin Austin TX 78712 USA
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24
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Minoshima W, Masui K, Tani T, Nawa Y, Fujita S, Ishitobi H, Hosokawa C, Inouye Y. Deuterated Glutamate-Mediated Neuronal Activity on Micro-Electrode Arrays. MICROMACHINES 2020; 11:mi11090830. [PMID: 32878218 PMCID: PMC7569784 DOI: 10.3390/mi11090830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 08/28/2020] [Indexed: 11/16/2022]
Abstract
The excitatory synaptic transmission is mediated by glutamate in neuronal networks of the mammalian brain. In addition to the synaptic glutamate, extra-synaptic glutamate is known to modulate the neuronal activity. In neuronal networks, glutamate uptake is an important role of neurons and glial cells for lowering the concentration of extracellular glutamate and to avoid the excitotoxicity by glutamate. Monitoring the spatial distribution of intracellular glutamate is important to study the uptake of glutamate, but the approach has been hampered by the absence of appropriate glutamate analogs that report the localization of glutamate. Deuterium-labeled glutamate (GLU-D) is a promising tracer for monitoring the intracellular concentration of glutamate, but physiological properties of GLU-D have not been studied. Here we study the effects of extracellular GLU-D for the neuronal activity by using primary cultured rat hippocampal neurons that form neuronal networks on microelectrodes array. The frequency of firing in the spontaneous activity of neurons increased with the increasing concentration of extracellular GLU-D. The frequency of synchronized burst activity in neurons increased similarly as we observed in the spontaneous activity. These changes of the neuronal activity with extracellular GLU-D were suppressed by antagonists of glutamate receptors. These results suggest that GLU-D can be used as an analog of glutamate with equivalent effects for facilitating the neuronal activity. We anticipate GLU-D developing as a promising analog of glutamate for studying the dynamics of glutamate during neuronal activity.
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Affiliation(s)
- Wataru Minoshima
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Kyoko Masui
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Tomomi Tani
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda 563-0026, Japan;
| | - Yasunori Nawa
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Satoshi Fujita
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ikeda 563-0026, Japan;
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Hidekazu Ishitobi
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
| | - Chie Hosokawa
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Department of Chemistry, Division of Molecular Materials Science, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan
- Correspondence: (C.H.); (Y.I.); Tel.: +81-6-6605-3700 (C.H.); +81-6-6879-4615 (Y.I.)
| | - Yasushi Inouye
- AIST–Osaka University Advanced Photonics and Biosensing Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, AIST, Osaka 565-0871, Japan; (W.M.); (K.M.); (Y.N.); (S.F.); (H.I.)
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
- Correspondence: (C.H.); (Y.I.); Tel.: +81-6-6605-3700 (C.H.); +81-6-6879-4615 (Y.I.)
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25
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Zhao Z, Chen C, Xiong H, Ji J, Min W. Metabolic Activity Phenotyping of Single Cells with Multiplexed Vibrational Probes. Anal Chem 2020; 92:9603-9612. [PMID: 32530266 DOI: 10.1021/acs.analchem.0c00790] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Quantitative measurements of metabolic activities of individual cells are essential to understanding questions in diverse fields in biology. To address this challenge, we present a method, termed metabolic activity phenotyping (MAP), to probe metabolic fluxes by utilizing multiplexed vibrational metabolic probes. With specifically designed single-whole-cell confocal micro-Raman spectroscopy, quantitative measurement of lipid and protein synthesis activity was achieved with high throughput (several orders of magnitude improvement over a commercial confocal system). In addition, metabolic heterogeneity upon various drug treatments was also revealed and evaluated at the single-cell level. We further demonstrated that MAP was more robust than the label-free Raman methods and was able to make the correct classification among diverse cancer types and breast cancer subtypes by exploring the dimension of metabolism. The capability of MAP to explore metabolic profiles at the single-cell level makes it a valuable tool for basic single-cell studies as well as other screening applications.
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Affiliation(s)
- Zhilun Zhao
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Chen Chen
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Hanqing Xiong
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Jingwei Ji
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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26
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Wang Y, Xu J, Kong L, Li B, Li H, Huang WE, Zheng C. Raman-activated sorting of antibiotic-resistant bacteria in human gut microbiota. Environ Microbiol 2020; 22:2613-2624. [PMID: 32114713 PMCID: PMC7383503 DOI: 10.1111/1462-2920.14962] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/26/2020] [Indexed: 01/12/2023]
Abstract
The antibiotic‐resistant bacteria (ARB) and antibiotic‐resistant genes (ARGs) in human gut microbiota have significant impact on human health. While high throughput metagenomic sequencing reveals genotypes of microbial communities, the functionality, phenotype and heterogeneity of human gut microbiota are still elusive. In this study, we applied Raman microscopy and deuterium isotope probing (Raman–DIP) to detect metabolic active ARB (MA‐ARB) in situ at the single‐cell level in human gut microbiota from two healthy adults. We analysed the relative abundances of MA‐ARB under different concentrations of amoxicillin, cephalexin, tetracycline, florfenicol and vancomycin. To establish the link between phenotypes and genotypes of the MA‐ARB, Raman‐activated cell sorting (RACS) was used to sort MA‐ARB from human gut microbiota, and mini‐metagenomic DNA of the sorted bacteria was amplified, sequenced and analysed. The sorted MA‐ARB and their associated ARGs were identified. Our results suggest a strong relation between ARB in human gut microbiota and personal medical history. This study demonstrates that the toolkit of Raman–DIP, RACS and DNA sequencing can be useful to unravel both phenotypes and genotypes of ARB in human gut 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
| | - Bei Li
- The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, CAS, 130033, Changchun, China.,HOOKE Instruments Ltd., 130033, Changchun, China
| | - Hang Li
- HOOKE Instruments Ltd., 130033, Changchun, 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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27
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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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28
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Phelan J, Altharawi A, Chan KLA. Tracking glycosylation in live cells using FTIR spectroscopy. Talanta 2020; 211:120737. [PMID: 32070609 DOI: 10.1016/j.talanta.2020.120737] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/09/2020] [Accepted: 01/11/2020] [Indexed: 12/13/2022]
Abstract
This is the first demonstration of the study of glycan protein turnover in living cells by FTIR with commercially available tetraacetylated N-Azidoacetyl-D-Mannosamine (Ac4ManNAz) label. The FTIR analysis has shown to be able to monitor the metabolism of glycans in living cells in real time. The method is simple, quantitative and requires equipment that are available in many laboratories. It can be used in a wide range of applications such as the study of glycosylation and cell-signalling.
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Affiliation(s)
- Joshua Phelan
- Institute of Pharmaceutical Science, King's College London, SE1 9NH, UK; Biological Science, College of Natural Sciences and Mathematics, California State University Fullerton, USA
| | - Ali Altharawi
- Institute of Pharmaceutical Science, King's College London, SE1 9NH, UK
| | - K L Andrew Chan
- Institute of Pharmaceutical Science, King's College London, SE1 9NH, UK.
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29
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Yonamine Y, Hiramatsu K, Ideguchi T, Ito T, Fujiwara T, Miura Y, Goda K, Hoshino Y. Spatiotemporal monitoring of intracellular metabolic dynamics by resonance Raman microscopy with isotope labeling. RSC Adv 2020; 10:16679-16686. [PMID: 35498863 PMCID: PMC9053077 DOI: 10.1039/d0ra02803g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023] Open
Abstract
We probed production process of a cellular metabolite with a stable isotope-labeled substrate exposed to various conditions.
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Affiliation(s)
- Yusuke Yonamine
- Research Institute for Electronic Science
- Hokkaido University
- Sapporo 001-0021
- Japan
| | - Kotaro Hiramatsu
- Department of Chemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- Research Centre for Spectrochemistry
| | - Takuro Ideguchi
- Research Centre for Spectrochemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- PRESTO
| | - Takuro Ito
- Japan Science and Technology Agency
- Kawaguchi-shi
- Japan
| | - Tomomi Fujiwara
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Yoshiko Miura
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Keisuke Goda
- Department of Chemistry
- The University of Tokyo
- Tokyo 113-0033
- Japan
- Japan Science and Technology Agency
| | - Yu Hoshino
- Department of Chemical Engineering
- Kyushu University
- Fukuoka 819-0395
- Japan
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30
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Turk N, Demol H, Skirtach A, Baets R, Gevaert K. Towards SERS-based multiplexed monitoring of protease activity using non-natural aromatic amino acids. EPJ WEB OF CONFERENCES 2020. [DOI: 10.1051/epjconf/202023804001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Surface Enhanced Raman Spectroscopy (SERS) allows sensitive and selective detection of protease activity by monitoring the cleavage of specific peptide substrates. Furthermore, it offers the possibility for multiplexing, during which the activity of two (or more) proteases with different specificities is detected simultaneously. To distinguish between the contributions of different proteases, different aromatic amino acids with non-overlapping SERS peaks need to be used as Raman reporters. As the three natural aromatic amino acids only offer limited possibilities for multiplexing, we examined several non-natural aromatic amino acids with the aim of expanding multiplexing possibilities. We recorded their SERS spectra for the Raman shifts of 300-1700 cm–1 and identified their characteristic SERS peaks. Of the examined nonnatural aromatic amino acids, 3-nitro-tyrosine and two phenylalanines containing stable heavy isotopes seem particularly promising for multiplexing applications. Besides exhibiting characteristic SERS peaks in the spectral region of interest, these non-natural aromatics provide strong SERS peaks compared to natural aromatic amino acids, consequently improving detection sensitivity.
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31
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Zulick C, Kunapareddy N, Grun J. Isotope Identification Mechanisms Enabled by Swept-Wavelength Raman Spectroscopy. APPLIED SPECTROSCOPY 2020; 74:97-107. [PMID: 31710247 DOI: 10.1177/0003702819878232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Swept-wavelength Raman signatures have been measured for isotopic variants of polyethylene, acetic acid, and potassium sulfates. The swept-wavelength measurements produce two-dimensional Raman signatures which enable identification techniques based on changes in Raman peak amplitudes as a function of wavelength. In addition to the typical Raman peak energy shifts, which results from the change in isotope mass, three wavelength dependent mechanisms for isotope identification have been identified. Changes in the shape of the Raman signal, the presence and absence of Raman peaks over specific wavelength ranges, and changes in absorption of the Raman signal were observed as a result of isotopic substitution. These features provide additional specificity in the isotopic Raman signatures which suggests swept-wavelength Raman signatures will facilitate the identification of isotopes in complex and dirty mixtures. Measurements in the visible range suggest that the identification mechanisms are primarily evident in the ultraviolet, or resonance Raman, region.
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Affiliation(s)
- Calvin Zulick
- Plasma Physics Division, Naval Research Laboratory, Washington, USA
| | | | - Jacob Grun
- Plasma Physics Division, Naval Research Laboratory, Washington, USA
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32
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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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33
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Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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34
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Abstract
Imaging techniques greatly facilitate the comprehensive knowledge of biological systems. Although imaging methodology for biomacromolecules such as protein and nucleic acids has been long established, microscopic techniques and contrast mechanisms are relatively limited for small biomolecules, which are equally important participants in biological processes. Recent developments in Raman imaging, including both microscopy and tailored vibrational tags, have created exciting opportunities for noninvasive imaging of small biomolecules in living cells, tissues, and organisms. Here, we summarize the principle and workflow of small-biomolecule imaging by Raman microscopy. Then, we review recent efforts in imaging, for example, lipids, metabolites, and drugs. The unique advantage of Raman imaging has been manifested in a variety of applications that have provided novel biological insights.
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Affiliation(s)
- Yihui Shen
- Department of Chemistry, Columbia University, New York, NY 10027, USA;
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, NY 10027, USA;
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY 10027, USA;
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35
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Li X, Li Y, Jiang M, Wu W, He S, Chen C, Qin Z, Tang BZ, Mak HY, Qu JY. Quantitative Imaging of Lipid Synthesis and Lipolysis Dynamics in Caenorhabditis elegans by Stimulated Raman Scattering Microscopy. Anal Chem 2019; 91:2279-2287. [PMID: 30589537 DOI: 10.1021/acs.analchem.8b04875] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Quantitative methods to precisely measure cellular states in vivo have become increasingly important and desirable in modern biology. Recently, stimulated Raman scattering (SRS) microscopy has emerged as a powerful tool to visualize small biological molecules tagged with alkyne (C≡C) or carbon-deuterium (C-D) bonds in the cell-silent region. In this study, we developed a technique based on SRS microscopy of vibrational tags for quantitative imaging of lipid synthesis and lipolysis in live animals. The technique aims to overcome the major limitations of conventional fluorescent staining and lipid extraction methods that do not provide the capability of in vivo quantitative analysis. Specifically, we used three bioorthogonal lipid molecules (the alkyne-tagged fatty acid 17-ODYA, deuterium-labeled saturated fatty acid PA-D31, and unsaturated fatty acid OA-D34) to investigate the metabolic dynamics of lipid droplets (LDs) in live Caenorhabditis elegans ( C. elegans). Using a hyperspectral SRS (hsSRS) microscope and subtraction method, the interfering non-Raman background was eliminated to improve the accuracy of lipid quantification. A linear relationship between SRS signals and fatty acid molar concentrations was accurately established. With this quantitative analysis tool, we imaged and determined the changes in concentration of the three fatty acids in LDs of fed or starved adult C. elegans. Using the hsSRS imaging mode, we also observed the desaturation of fatty acids in adult C. elegans via spectral analysis on the SRS signals from LDs. The results demonstrated the unique capability of hsSRS microscopy in quantitative analysis of lipid metabolism in vivo.
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Affiliation(s)
- Xuesong Li
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Yan Li
- Division of Life Science , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Meijuan Jiang
- Department of Chemistry , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Wanjie Wu
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Sicong He
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Congping Chen
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Zhongya Qin
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Ben Zhong Tang
- Department of Chemistry , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Ho Yi Mak
- Division of Life Science , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
| | - Jianan Y Qu
- Department of Electronic and Computer Engineering , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China.,Center of Systems Biology and Human Health, School of Science and Institute for Advanced Study , Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , Hong Kong 999077 , China
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36
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Mochizuki M, Sato S, Asatyas S, Leśnikowski ZJ, Hayashi T, Nakamura H. Raman cell imaging with boron cluster molecules conjugated with biomolecules. RSC Adv 2019; 9:23973-23978. [PMID: 35530627 PMCID: PMC9069464 DOI: 10.1039/c9ra04228h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/28/2019] [Indexed: 01/03/2023] Open
Abstract
Raman spectroscopic measurements and theoretical calculation revealed that the Raman bands corresponding to the B–H stretching vibrations of two types of simple icosahedral boron clusters, ortho-carborane 3 and closo-dodecaborate 4 appeared at approximately 2450–2700 cm−1, and did not overlap with those of cellular components. Although ortho-carborane 3 possesses a possible property as a Raman probe, it was difficult to measure Raman imaging in the cell due to its poor water solubility. In fact, ortho-carborane derivative 6, which internally has an alkyne moiety, exhibited very weak Raman signals of the C
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C stretching and the B–H stretching vibrations were barely detected at a 400 ppm boron concentration in HeLa cells. In contrast, closo-dodecaborate derivatives such as BSH (5) were found to be a potential Raman imaging probe cluster for target molecules in the cell. BSH-conjugated cholesterol 7 (BSH-Chol) was synthesized and used in Raman imaging in cells. Raman imaging and spectral analysis revealed that BSH-based Raman tags provide a versatile platform for quantitative Raman imaging. We performed Raman cell imaging using boron clusters.![]()
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Affiliation(s)
- Masahito Mochizuki
- School of Materials and Chemical Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Shinichi Sato
- Laboratory of Chemical and Life Science Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8502
- Japan
| | - Syifa Asatyas
- School of Materials and Chemical Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | | | - Tomohiro Hayashi
- School of Materials and Chemical Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
- JST-PRESTO
| | - Hiroyuki Nakamura
- Laboratory of Chemical and Life Science Innovative Research
- Tokyo Institute of Technology
- Yokohama 226-8502
- Japan
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37
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Xu J, Zhu D, Ibrahim AD, Allen CCR, Gibson CM, Fowler PW, Song Y, Huang WE. Raman Deuterium Isotope Probing Reveals Microbial Metabolism at the Single-Cell Level. Anal Chem 2017; 89:13305-13312. [DOI: 10.1021/acs.analchem.7b03461] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jiabao Xu
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Di Zhu
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
| | - Aliyu D. Ibrahim
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | - Christopher C. R. Allen
- School of Biological Sciences & Institute for Global Food Security, Queen’s University Belfast, Belfast BT9 7BL, United Kingdom
| | | | - Patrick W. Fowler
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom
| | - Yizhi Song
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
| | - Wei E. Huang
- Department
of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
- Kroto
Research Institute, University of Sheffield, Sheffield S3 7HQ, United Kingdom
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38
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Fleissner F, Pütz S, Schwendy M, Bonn M, Parekh SH. Measuring Intracellular Secondary Structure of a Cell-Penetrating Peptide in Situ. Anal Chem 2017; 89:11310-11317. [DOI: 10.1021/acs.analchem.7b01895] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Frederik Fleissner
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Sabine Pütz
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Mischa Schwendy
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Mischa Bonn
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
| | - Sapun H. Parekh
- Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, D-55128 Mainz, Germany
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39
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Zhao Z, Shen Y, Hu F, Min W. Applications of vibrational tags in biological imaging by Raman microscopy. Analyst 2017; 142:4018-4029. [PMID: 28875184 PMCID: PMC5674523 DOI: 10.1039/c7an01001j] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
As a superb tool to visualize and study the spatial-temporal distribution of chemicals, Raman microscopy has made a big impact in many disciplines of science. While label-free imaging has been the prevailing strategy in Raman microscopy, recent development and applications of vibrational/Raman tags, particularly when coupled with stimulated Raman scattering (SRS) microscopy, have generated intense excitement in biomedical imaging. SRS imaging of vibrational tags has enabled researchers to study a wide range of small biomolecules with high specificity, sensitivity and multiplex capability, at a single live cell level, tissue level or even in vivo. As reviewed in this article, this platform has facilitated imaging distribution and dynamics of small molecules such as glucose, lipids, amino acids, nucleic acids, and drugs that are otherwise difficult to monitor with other means. As both the vibrational tags and Raman instrumental development progress rapidly and synergistically, we anticipate that this technique will shed light onto an even broader spectrum of biomedical problems.
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Affiliation(s)
- Zhilun Zhao
- Department of Chemistry, Columbia University, New York, 10027, USA.
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40
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Yonamine Y, Suzuki Y, Ito T, Miura Y, Goda K, Ozeki Y, Hoshino Y. Monitoring Photosynthetic Activity in Microalgal Cells by Raman Spectroscopy with Deuterium Oxide as a Tracking Probe. Chembiochem 2017; 18:2063-2068. [DOI: 10.1002/cbic.201700314] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Yusuke Yonamine
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
| | - Yuta Suzuki
- Department of Electrical Engineering and Information Systems; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Takuro Ito
- Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan
| | - Yoshiko Miura
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
| | - Keisuke Goda
- Japan Science and Technology Agency; 4-1-8 Honcho Kawaguchi-shi Saitama 332-0012 Japan
- Department of Chemistry; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Department of Electrical Engineering; University of California; 420 Westwood Plaza Los Angeles CA 90095 USA
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems; University of Tokyo; 7-3-1 Hongo Bunkyo-ku Tokyo 113-8656 Japan
| | - Yu Hoshino
- Department of Chemical Engineering; Kyushu University; 744 Motooka Fukuoka 819-0395 Japan
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41
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Relevant aspects of unmixing/resolution analysis for the interpretation of biological vibrational hyperspectral images. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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42
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Semerdzhiev SA, Shvadchak VV, Subramaniam V, Claessens MMAE. Non-uniform self-assembly: On the anisotropic architecture of α-synuclein supra-fibrillar aggregates. Sci Rep 2017; 7:7699. [PMID: 28794461 PMCID: PMC5550477 DOI: 10.1038/s41598-017-06532-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/14/2017] [Indexed: 11/09/2022] Open
Abstract
Although the function of biopolymer hydrogels in nature depends on structural anisotropy at mesoscopic length scales, the self-assembly of such anisotropic structures in vitro is challenging. Here we show that fibrils of the protein α-synuclein spontaneously self-assemble into structurally anisotropic hydrogel particles. While the fibrils in the interior of these supra-fibrillar aggregates (SFAs) are randomly oriented, the fibrils in the periphery prefer to cross neighboring fibrils at high angles. This difference in organization coincides with a significant difference in polarity of the environment in the central and peripheral parts of the SFA. We rationalize the structural anisotropy of SFAs in the light of the observation that αS fibrils bind a substantial amount of counterions. We propose that, with the progress of protein polymerization into fibrils, this binding of counterions changes the ionic environment which triggers a change in fibril organization resulting in anisotropy in the architecture of hydrogel particles.
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Affiliation(s)
- Slav A Semerdzhiev
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
| | - Volodymyr V Shvadchak
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, 166-10, Czech Republic
| | - Vinod Subramaniam
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081, HV, Amsterdam, The Netherlands
| | - Mireille M A E Claessens
- Nanobiophysics group, MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500, AE, Enschede, The Netherlands.
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43
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Sobot D, Mura S, Rouquette M, Vukosavljevic B, Cayre F, Buchy E, Pieters G, Garcia-Argote S, Windbergs M, Desmaële D, Couvreur P. Circulating Lipoproteins: A Trojan Horse Guiding Squalenoylated Drugs to LDL-Accumulating Cancer Cells. Mol Ther 2017; 25:1596-1605. [PMID: 28606375 PMCID: PMC5498828 DOI: 10.1016/j.ymthe.2017.05.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/30/2022] Open
Abstract
Selective delivery of anticancer drugs to rapidly growing cancer cells can be achieved by taking advantage of their high receptor-mediated uptake of low-density lipoproteins (LDLs). Indeed, we have recently discovered that nanoparticles made of the squalene derivative of the anticancer agent gemcitabine (SQGem) strongly interacted with the LDLs in the human blood. In the present study, we showed both in vitro and in vivo that such interaction led to the preferential accumulation of SQGem in cancer cells (MDA-MB-231) with high LDL receptor expression. As a result, an improved pharmacological activity has been observed in MDA-MB-231 tumor-bearing mice, an experimental model with a low sensitivity to gemcitabine. Accordingly, we proved that the use of squalene moieties not only induced the gemcitabine insertion into lipoproteins, but that it could also be exploited to indirectly target cancer cells in vivo.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/pathology
- Adenocarcinoma/therapy
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Breast Neoplasms/therapy
- Cell Line, Tumor
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/chemistry
- Deoxycytidine/pharmacology
- Drug Carriers
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lipoproteins, LDL/chemistry
- Lipoproteins, LDL/metabolism
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Nude
- Mice, SCID
- Nanoparticles/administration & dosage
- Nanoparticles/chemistry
- Receptors, LDL/genetics
- Receptors, LDL/metabolism
- Squalene/chemistry
- Tumor Burden/drug effects
- Xenograft Model Antitumor Assays
- Gemcitabine
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Affiliation(s)
- Dunja Sobot
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Simona Mura
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Marie Rouquette
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Branko Vukosavljevic
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Campus E8 1, 66123 Saarbruecken, Germany
| | - Fanny Cayre
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Eric Buchy
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Grégory Pieters
- SCBM, CEA, Université Paris Saclay, LabEx LERMIT, 91191 Gif-sur-Yvette, France
| | | | - Maike Windbergs
- Department of Drug Delivery, Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, Campus E8 1, 66123 Saarbruecken, Germany; Institute of Pharmaceutical Technology, Buchmann Institute for Molecular Life Sciences, Goethe University, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany
| | - Didier Desmaële
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Patrick Couvreur
- Institut Galien Paris-Sud, UMR 8612, CNRS, University Paris-Sud, Université Paris-Saclay, Faculté de Pharmacie, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France.
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44
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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45
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Abstract
Stimulated Raman scattering (SRS) describes a family of techniques first discovered and developed in the 1960s. Whereas the nascent history of the technique is parallel to that of laser light sources, recent advances have spurred a resurgence in its use and development that has spanned across scientific fields and spatial scales. SRS is a nonlinear technique that probes the same vibrational modes of molecules that are seen in spontaneous Raman scattering. While spontaneous Raman scattering is an incoherent technique, SRS is a coherent process, and this fact provides several advantages over conventional Raman techniques, among which are much stronger signals and the ability to time-resolve the vibrational motions. Technological improvements in pulse generation and detection strategies have allowed SRS to probe increasingly smaller volumes and shorter time scales. This has enabled SRS research to move from its original domain, of probing bulk media, to imaging biological tissues and single cells at the micro scale, and, ultimately, to characterizing samples with subdiffraction resolution at the nanoscale. In this Review, we give an overview of the history of the technique, outline its basic properties, and present historical and current uses at multiple length scales to underline the utility of SRS to the molecular sciences.
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Affiliation(s)
- Richard C Prince
- Department of Biomedical Engineering, University of California, Irvine , 1436 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis , B-18, 139 Smith Hall, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Eric O Potma
- Department of Chemistry, University of California, Irvine , 1107 Natural Sciences II, Irvine, California 92697-2025, United States
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46
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Wei L, Hu F, Chen Z, Shen Y, Zhang L, Min W. Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes. Acc Chem Res 2016; 49:1494-502. [PMID: 27486796 PMCID: PMC5704954 DOI: 10.1021/acs.accounts.6b00210] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Innovations in light microscopy have tremendously revolutionized the way researchers study biological systems with subcellular resolution. In particular, fluorescence microscopy with the expanding choices of fluorescent probes has provided a comprehensive toolkit to tag and visualize various molecules of interest with exquisite specificity and high sensitivity. Although fluorescence microscopy is currently the method of choice for cellular imaging, it faces fundamental limitations for studying the vast number of small biomolecules. This is because common fluorescent labels, which are relatively bulky, could introduce considerable perturbation to or even completely alter the native functions of vital small biomolecules. Hence, despite their immense functional importance, these small biomolecules remain largely undetectable by fluorescence microscopy. To address this challenge, a bioorthogonal chemical imaging platform has recently been introduced. By coupling stimulated Raman scattering (SRS) microscopy, an emerging nonlinear Raman microscopy technique, with tiny and Raman-active vibrational probes (e.g., alkynes and stable isotopes), bioorthogonal chemical imaging exhibits superb sensitivity, specificity, and biocompatibility for imaging small biomolecules in live systems. In this Account, we review recent technical achievements for visualizing a broad spectrum of small biomolecules, including ribonucleosides and deoxyribonucleosides, amino acids, fatty acids, choline, glucose, cholesterol, and small-molecule drugs in live biological systems ranging from individual cells to animal tissues and model organisms. Importantly, this platform is compatible with live-cell biology, thus allowing real-time imaging of small-molecule dynamics. Moreover, we discuss further chemical and spectroscopic strategies for multicolor bioorthogonal chemical imaging, a valuable technique in the era of "omics". As a unique tool for biological discovery, this platform has been applied to studying various metabolic processes under both physiological and pathological states, including protein synthesis activity of neuronal systems, protein aggregations in Huntington disease models, glucose uptake in tumor xenografts, and drug penetration through skin tissues. We envision that the coupling of SRS microscopy with vibrational probes would do for small biomolecules what fluorescence microscopy of fluorophores has done for larger molecular species.
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Affiliation(s)
- Lu Wei
- Department of Chemistry, Columbia University, New York, 10027
| | - Fanghao Hu
- Department of Chemistry, Columbia University, New York, 10027
| | - Zhixing Chen
- Department of Chemistry, Columbia University, New York, 10027
| | - Yihui Shen
- Department of Chemistry, Columbia University, New York, 10027
| | - Luyuan Zhang
- Department of Chemistry, Columbia University, New York, 10027
| | - Wei Min
- Department of Chemistry, Columbia University, New York, 10027
- Kavli Institute for Brain Science, Columbia University, New York, 10027
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47
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Kumar B. N. V, Guo S, Bocklitz T, Rösch P, Popp J. Demonstration of Carbon Catabolite Repression in Naphthalene Degrading Soil Bacteria via Raman Spectroscopy Based Stable Isotope Probing. Anal Chem 2016; 88:7574-82. [DOI: 10.1021/acs.analchem.6b01046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Vinay Kumar B. N.
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Shuxia Guo
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Thomas Bocklitz
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
| | - Petra Rösch
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
| | - Jürgen Popp
- Institute
of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University of Jena, Helmholtzweg 4, D-07743 Jena, Germany
- InfectoGnostics, Forschungscampus Jena, Philosophenweg
7, D-07743 Jena, Germany
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, D-07745 Jena, Germany
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48
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Wang Y, Huang WE, Cui L, Wagner M. Single cell stable isotope probing in microbiology using Raman microspectroscopy. Curr Opin Biotechnol 2016; 41:34-42. [PMID: 27149160 DOI: 10.1016/j.copbio.2016.04.018] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 02/17/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
Microbial communities are essential for most ecosystem processes and interact in highly complex ways with virtually all eukaryotes. Thus, a detailed understanding of the function of such communities is a fundamental prerequisite for microbial ecologists, applied microbiologists and microbiome researchers. Using single cell Raman microspectroscopy, biochemical fingerprints of individual microbial cells can be obtained in an externally label-free and non-destructive manner. If combined with stable isotope probing (SIP), Raman spectroscopy can directly reveal functions of single microorganisms in their natural habitat. This review provides an update on various SIP-approaches suitable for combination with different Raman scattering techniques and illustrates how single cell Raman SIP can be directly combined with the omics-centric analysis pipelines to investigate microbial communities.
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Affiliation(s)
- Yun Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics and Single Cell Center, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, PR China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Michael Wagner
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network 'Chemistry Meets Microbiology', University of Vienna, 1090 Vienna, Austria
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49
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Tipping WJ, Lee M, Serrels A, Brunton VG, Hulme AN. Stimulated Raman scattering microscopy: an emerging tool for drug discovery. Chem Soc Rev 2016; 45:2075-89. [PMID: 26839248 PMCID: PMC4839273 DOI: 10.1039/c5cs00693g] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Indexed: 12/26/2022]
Abstract
Optical microscopy techniques have emerged as a cornerstone of biomedical research, capable of probing the cellular functions of a vast range of substrates, whilst being minimally invasive to the cells or tissues of interest. Incorporating biological imaging into the early stages of the drug discovery process can provide invaluable information about drug activity within complex disease models. Spontaneous Raman spectroscopy has been widely used as a platform for the study of cells and their components based on chemical composition; but slow acquisition rates, poor resolution and a lack of sensitivity have hampered further development. A new generation of stimulated Raman techniques is emerging which allows the imaging of cells, tissues and organisms at faster acquisition speeds, and with greater resolution and sensitivity than previously possible. This review focuses on the development of stimulated Raman scattering (SRS), and covers the use of bioorthogonal tags to enhance sample detection, and recent applications of both spontaneous Raman and SRS as novel imaging platforms to facilitate the drug discovery process.
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Affiliation(s)
- W. J. Tipping
- EaStCHEM School of Chemistry , The University of Edinburgh , Joseph Black Building , David Brewster Road , Edinburgh , EH9 3FJ , UK .
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - M. Lee
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - A. Serrels
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - V. G. Brunton
- Edinburgh Cancer Research Centre , Institute of Genetics and Molecular Medicine , The University of Edinburgh , Crewe Road South , Edinburgh , EH4 2XR , UK
| | - A. N. Hulme
- EaStCHEM School of Chemistry , The University of Edinburgh , Joseph Black Building , David Brewster Road , Edinburgh , EH9 3FJ , UK .
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50
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Huleihel M, Shufan E, Zeiri L, Salman A. Detection of Vero Cells Infected with Herpes Simplex Types 1 and 2 and Varicella Zoster Viruses Using Raman Spectroscopy and Advanced Statistical Methods. PLoS One 2016; 11:e0153599. [PMID: 27078266 PMCID: PMC4831712 DOI: 10.1371/journal.pone.0153599] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 03/31/2016] [Indexed: 12/17/2022] Open
Abstract
Of the eight members of the herpes family of viruses, HSV1, HSV2, and varicella zoster are the most common and are mainly involved in cutaneous disorders. These viruses usually are not life-threatening, but in some cases they might cause serious infections to the eyes and the brain that can lead to blindness and possibly death. An effective drug (acyclovir and its derivatives) is available against these viruses. Therefore, early detection and identification of these viral infections is highly important for an effective treatment. Raman spectroscopy, which has been widely used in the past years in medicine and biology, was used as a powerful spectroscopic tool for the detection and identification of these viral infections in cell culture, due to its sensitivity, rapidity and reliability. Our results showed that it was possible to differentiate, with a 97% identification success rate, the uninfected Vero cells that served as a control, from the Vero cells that were infected with HSV-1, HSV-2, and VZV. For that, linear discriminant analysis (LDA) was performed on the Raman spectra after principal component analysis (PCA) with a leave one out (LOO) approach. Raman spectroscopy in tandem with PCA and LDA enable to differentiate among the different herpes viral infections of Vero cells in time span of few minutes with high accuracy rate. Understanding cell molecular changes due to herpes viral infections using Raman spectroscopy may help in early detection and effective treatment.
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Affiliation(s)
- Mahmoud Huleihel
- Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- * E-mail: (AS); (MH)
| | - Elad Shufan
- Department of Physics, SCE- Shamoon College of Engineering, Beer-Sheva, Israel
| | - Leila Zeiri
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ahmad Salman
- Department of Physics, SCE- Shamoon College of Engineering, Beer-Sheva, Israel
- * E-mail: (AS); (MH)
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