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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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2
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Zheltikov AM. Thermal and Quantum Barrier Passage as Potential-Driven Markovian Dynamics. J Phys Chem B 2023; 127:9413-9422. [PMID: 37905974 PMCID: PMC10863070 DOI: 10.1021/acs.jpcb.3c02744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/08/2023] [Indexed: 11/02/2023]
Abstract
Rapidly progressing laser technologies provide powerful tools to study potential barrier-passage dynamics in physical, chemical, and biological systems with unprecedented temporal and spatial resolution and a remarkable chemical and structural specificity. The available theories of barrier passage, however, operate with equations, potentials, and parameters that are best suited for a specific area of research and a specific class of systems and processes. Making connections among these theories is often anything but easy. Here, we address this problem by presenting a unified framework for the description of a vast variety of classical and quantum barrier-passage phenomena, revealing an innate connection between various types of barrier-passage dynamics and providing closed-form equations showing how the signature exponentials in classical and quantum barrier-passage rates relate to and translate into each other. In this framework, the Arrhenius-law kinetics, the emergence of the Gibbs distribution, Hund's molecular wave-packet well-to-well oscillatory dynamics, Keldysh photoionization, and Kramers' escape over a potential barrier are all understood as manifestations of a potential-driven Markovian dynamics whereby a system evolves from a state of local stability. Key to the irreducibility of quantum tunneling to thermally activated barrier passage is the difference in the ways the diffusion-driving potentials emerge in these two tunneling settings, giving rise to stationary states with a distinctly different structure.
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Affiliation(s)
- A. M. Zheltikov
- Institute for Quantum Science and Engineering,
Department of Physics and Astronomy, Texas
A&M University, College Station, Texas 77843, United States
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3
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Zachleder V, Vítová M, Hlavová M, Moudříková Š, Mojzeš P, Heumann H, Becher JR, Bišová K. Stable isotope compounds - production, detection, and application. Biotechnol Adv 2018; 36:784-797. [PMID: 29355599 DOI: 10.1016/j.biotechadv.2018.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/14/2022]
Abstract
Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.
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Affiliation(s)
- Vilém Zachleder
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Milada Vítová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Monika Hlavová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Šárka Moudříková
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | | | | | - Kateřina Bišová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic.
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Pacia MZ, Turnau K, Baranska M, Kaczor A. Interplay between carotenoids, hemoproteins and the “life band” origin studied in live Rhodotorula mucilaginosa cells by means of Raman microimaging. Analyst 2015; 140:1809-13. [DOI: 10.1039/c4an01787k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Raman microimaging of live Rhodotorula mucilaginosa cells enabled the interrelation of carotenoids, hemoproteins and the unknown species related to the “Raman signature of life”.
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Affiliation(s)
- Marta Z. Pacia
- Faculty of Chemistry
- Jagiellonian University
- 30-060 Krakow
- Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)
| | - Katarzyna Turnau
- Institute of Environmental Sciences and Malopolska Centre of Biotechnology
- Jagiellonian University
- 30-387 Krakow
- Poland
| | - Malgorzata Baranska
- Faculty of Chemistry
- Jagiellonian University
- 30-060 Krakow
- Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)
| | - Agnieszka Kaczor
- Faculty of Chemistry
- Jagiellonian University
- 30-060 Krakow
- Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET)
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Photobleaching of the resonance Raman lines of cytochromes in living yeast cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:269-74. [PMID: 25463677 DOI: 10.1016/j.jphotobiol.2014.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 10/11/2014] [Indexed: 01/25/2023]
Abstract
The photobleaching of the resonance cytochrome Raman lines in living Saccharomyces cerevisiae cells was studied. The photobleaching rate versus the irradiation power was described by square function plus a constant in contrast to the linear dependence of the photoinjury rate. This difference distinguishes the cytochrome photooxidation from other processes of the cell photodamage. The square dependence is associated with the reaction involving two photogenerated intermediates while the constant with the dark redox balance rates. This work demonstrates a potential of Raman spectroscopy to characterize the native cytochrome reaction rates and to study the cell photodamage precursors.
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Molecular imaging of live cells by Raman microscopy. Curr Opin Chem Biol 2013; 17:708-15. [DOI: 10.1016/j.cbpa.2013.05.021] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/30/2013] [Accepted: 05/17/2013] [Indexed: 01/11/2023]
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Kaliaperumal V, Hamaguchi HO. Casting new physicochemical light on the fundamental biological processes in single living cells by using Raman microspectroscopy. CHEM REC 2012; 12:567-80. [PMID: 23129551 DOI: 10.1002/tcr.201200008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Indexed: 12/12/2022]
Abstract
This Personal Account highlights the capabilities of spontaneous Raman microspectroscopy for studying fundamental biological processes in a single living cell. Raman microspectroscopy provides time- and space-resolved vibrational Raman spectra that contain detailed information on the structure and dynamics of biomolecules in a cell. By using yeast as a model system, we have made great progress in the development of this methodology. The results that we have obtained so far are described herein with an emphasis placed on how three cellular processes, that is, cell-division, respiration, and cell-death, are traced and elucidated with the use of time- and space-resolved structural information that is extracted from the Raman spectra. For cell-division, compositional- and structural changes of various biomolecules are observed during the course of the whole cell cycle. For respiration, the redox state of mitochondrial cytochromes, which is inferred from the resonance Raman bands of cytochromes, is used to evaluate the respiration activity of a single cell, as well as that of isolated mitochondrial particles. Special reference is made to the "Raman spectroscopic signature of life", which is a characteristic Raman band at 1602 cm(-1) that is found in yeast cells. This signature reflects the cellular metabolic activity and may serve as a measure of mitochondrial dysfunction. For cell-death, "cross-talk" between the mitochondria and the vacuole in a dying cell is suggested.
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Affiliation(s)
- Venkatesh Kaliaperumal
- Department of Chemistry, School of Science, The University of Tokyo, Hongo 7-3-1 Tokyo,113-0033, Japan
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Noothalapati Venkata H, Shigeto S. Stable Isotope-Labeled Raman Imaging Reveals Dynamic Proteome Localization to Lipid Droplets in Single Fission Yeast Cells. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.chembiol.2012.08.020] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Chiu LD, Hullin-Matsuda F, Kobayashi T, Torii H, Hamaguchi HO. On the origin of the 1602 cm-1 Raman band of yeasts; contribution of ergosterol. JOURNAL OF BIOPHOTONICS 2012; 5:724-728. [PMID: 22529062 DOI: 10.1002/jbio.201200020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 03/05/2012] [Accepted: 03/12/2012] [Indexed: 05/31/2023]
Abstract
The 1602 cm(-1) Raman signature, which we call the "Raman spectroscopic signature of life" in yeasts, is a marker Raman band for cell metabolic activity. Despite the established fact that its intensity sensitively reflects the metabolic status of the cell, its molecular origin remained unclear. In this work, we propose ergosterol as the major contributor of the 1602 cm(-1) Raman signature. The theoretical isotope shift calculation for ergosterol agreed with previous observations. Furthermore, experiments showed that the Raman spectrum of ergosterol corresponds very well with the depleting spectral component in yeast that behaves together with the 1602 cm(-1) signature when the cells are under stress. This work implies that the 1602 cm(-1) Raman signature could serve as an intrinsic ergosterol marker in yeasts for the study of sterol metabolism in vivo and in a label-free manner, which could not be done by any other techniques at the current stage.
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Affiliation(s)
- Liang-da Chiu
- Department of Chemistry, School of Science, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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Huang CK, Ando M, Hamaguchi HO, Shigeto S. Disentangling dynamic changes of multiple cellular components during the yeast cell cycle by in vivo multivariate Raman imaging. Anal Chem 2012; 84:5661-8. [PMID: 22686107 DOI: 10.1021/ac300834f] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cellular processes are intrinsically complex and dynamic, in which a myriad of cellular components including nucleic acids, proteins, membranes, and organelles are involved and undergo spatiotemporal changes. Label-free Raman imaging has proven powerful for studying such dynamic behaviors in vivo and at the molecular level. To construct Raman images, univariate data analysis has been commonly employed, but it cannot be free from uncertainties due to severely overlapped spectral information. Here, we demonstrate multivariate curve resolution analysis for time-lapse Raman imaging of a single dividing yeast cell. A four-dimensional (spectral variable, spatial positions in the two-dimensional image plane, and time sequence) Raman data "hypercube" is unfolded to a two-way array and then analyzed globally using multivariate curve resolution. The multivariate Raman imaging thus accomplished successfully disentangles dynamic changes of both concentrations and distributions of major cellular components (lipids, proteins, and polysaccharides) during the cell cycle of the yeast cell. The results show a drastic decrease in the amount of lipids by ~50% after cell division and uncover a protein-associated component that has not been detected with previous univariate approaches.
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Affiliation(s)
- Chuan-Keng Huang
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu 30010, Taiwan
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Drescher D, Kneipp J. Nanomaterials in complex biological systems: insights from Raman spectroscopy. Chem Soc Rev 2012; 41:5780-99. [DOI: 10.1039/c2cs35127g] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Chiu LD, Hamaguchi HO. The "Raman spectroscopic signature of life" is closely related to haem function in budding yeasts. JOURNAL OF BIOPHOTONICS 2011; 4:30-33. [PMID: 20391543 DOI: 10.1002/jbio.201000029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 03/16/2010] [Accepted: 03/24/2010] [Indexed: 05/29/2023]
Abstract
HEM1 gene encodes δ-aminolevulinate synthase that is required for haem synthesis. It is an essential gene for yeast survival. The Raman spectra of HEM1 knockout (hem1Δ) yeast cells lacks a Raman band at 1602 cm(-1) that has been shown to reflect cell metabolic activity. This result suggests that the molecule giving rise to the"Raman spectroscopic signature of life" is closely related to haem functions in the cell. High amount of squalene is also observed in the hem1Δ strain, which is another new discovery of this study.
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Affiliation(s)
- Liang-da Chiu
- Department of Chemistry, the University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
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Okuno M, Kano H, Leproux P, Couderc V, Day J, Bonn M, Hamaguchi HO. Quantitative CARS Molecular Fingerprinting of Single Living Cells with the Use of the Maximum Entropy Method. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001560] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Okuno M, Kano H, Leproux P, Couderc V, Day J, Bonn M, Hamaguchi HO. Quantitative CARS Molecular Fingerprinting of Single Living Cells with the Use of the Maximum Entropy Method. Angew Chem Int Ed Engl 2010; 49:6773-7. [DOI: 10.1002/anie.201001560] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Onogi C, Hamaguchi HO. In Vivo Resonance Raman Detection of Ferrous Cytochromecfrom Mitochondria of Single Living Yeast Cells. CHEM LETT 2010. [DOI: 10.1246/cl.2010.270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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