51
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Ramirez JA, Posada JM, Handa IT, Hoch G, Vohland M, Messier C, Reu B. Near‐infrared spectroscopy (
NIRS
) predicts non‐structural carbohydrate concentrations in different tissue types of a broad range of tree species. Methods Ecol Evol 2015. [DOI: 10.1111/2041-210x.12391] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jorge A. Ramirez
- Center for Forest Research Université du Québec à Montréal P.O. Box 8888 Succursale Centre‐ville Montréal QC H3C 3P8 Canada
| | - Juan M. Posada
- Facultad de Ciencias Naturales y Matemáticas Universidad del Rosario Carrera 24 No. 63C‐69 Bogotá Colombia
| | - I. Tanya Handa
- Center for Forest Research Université du Québec à Montréal P.O. Box 8888 Succursale Centre‐ville Montréal QC H3C 3P8 Canada
| | - Günter Hoch
- Department of Environmental Sciences ‐ Botany University of Basel Schönbeinstrasse 6 4056 Basel Switzerland
| | - Michael Vohland
- Geoinformatics and Remote Sensing Institute for Geography University of Leipzig Johannisallee 19a 04103 Leipzig Germany
| | - Christian Messier
- Center for Forest Research Université du Québec à Montréal P.O. Box 8888 Succursale Centre‐ville Montréal QC H3C 3P8 Canada
- Departement des sciences naturelles and Institut des sciences de la foret temperee (ISFORT) Universite du Quebec en Outaouais 58 rue Principale Ripon QC J0V 1V0 Canada
| | - Björn Reu
- Institute of Biology University of Leipzig Johannisallee 21 04103 Leipzig Germany
- Escuela de Biología Universidad Industrial de Santander Cra. 27 Calle 9 UIS Edificio 45 Bucaramanga Colombia
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52
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Wang HF, Velarde L, Gan W, Fu L. Quantitative Sum-Frequency Generation Vibrational Spectroscopy of Molecular Surfaces and Interfaces: Lineshape, Polarization, and Orientation. Annu Rev Phys Chem 2015; 66:189-216. [DOI: 10.1146/annurev-physchem-040214-121322] [Citation(s) in RCA: 156] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hong-Fei Wang
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352;
| | - Luis Velarde
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260
| | - Wei Gan
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, Xinjiang 830011, China
| | - Li Fu
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352;
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53
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Han Y, Hsu J, Ge NH, Potma EO. Polarization-sensitive sum-frequency generation microscopy of collagen fibers. J Phys Chem B 2015; 119:3356-65. [PMID: 25614936 DOI: 10.1021/jp511058b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Point-scanning sum-frequency generation (SFG) microscopy enables the generation of images of collagen I fibers in tissues by tuning into specific vibrational resonances of the polypeptide. It is shown that when collagen-rich tissues are visualized near the 2954 cm(-1) stretching vibration of methylene groups, the SFG image contrast is higher compared to the contrast seen in nonresonant second-harmonic generation (SHG) imaging. Polarization and spectrally resolved analysis of the SFG signal as a function of fiber orientation in the CH-stretching range of the vibrational spectrum enabled a comparative characterization of the achiral tensor elements of collagen's second-order susceptibility. This analysis reveals that selected on-resonance tensor elements are enhanced over other elements, giving rise to a much stronger anisotropy ρ of the signal for SFG (ρ ≈ 15) compared to SHG (ρ ≈ 3). The improved anisotropy of the vibrationally resonant signal contributes to the higher contrast seen in the SFG tissue images.
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Affiliation(s)
- Yang Han
- Department of Chemistry, University of California at Irvine , Irvine, California 92697-2025, United States
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54
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Gallagher KL, Alfonso-Garcia A, Sanchez J, Potma EO, Santos GM. Plant growth conditions alter phytolith carbon. FRONTIERS IN PLANT SCIENCE 2015; 6:753. [PMID: 26442066 PMCID: PMC4585121 DOI: 10.3389/fpls.2015.00753] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 09/03/2015] [Indexed: 05/09/2023]
Abstract
Many plants, including grasses and some important human food sources, accumulate, and precipitate silica in their cells to form opaline phytoliths. These phytoliths contain small amounts of organic matter (OM) that are trapped during the process of silicification. Previous work has suggested that plant silica is associated with compounds such as proteins, lipids, lignin, and carbohydrate complexes. It is not known whether these compounds are cellular components passively encapsulated as the cell silicifies, polymers actively involved in the precipitation process or random compounds assimilated by the plant and discarded into a "glass wastebasket." Here, we used Raman spectroscopy to map the distribution of OM in phytoliths, and to analyze individual phytoliths isolated from Sorghum bicolor plants grown under different laboratory treatments. Using mapping, we showed that OM in phytoliths is distributed throughout the silica and is not related to dark spots visible in light microscopy, previously assumed to be the repository for phytolith OM. The Raman spectra exhibited common bands indicative of C-H stretching modes of general OM, and further more diagnostic bands consistent with carbohydrates, lignins, and other OM. These Raman spectra exhibited variability of spectral signatures and of relative intensities between sample treatments indicating that differing growth conditions altered the phytolith carbon. This may have strong implications for understanding the mechanism of phytolith formation, and for use of phytolith carbon isotope values in dating or paleoclimate reconstruction.
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Affiliation(s)
- Kimberley L Gallagher
- Department of Earth Systems Sciences, University of California, Irvine Irvine, CA, USA
| | - Alba Alfonso-Garcia
- Department of Biomedical Engineering, University of California, Irvine Irvine, CA, USA
| | - Jessica Sanchez
- Department of Biology, California State University of Fullerton Fullerton, CA, USA
| | - Eric O Potma
- Department of Chemistry, University of California, Irvine Irvine, CA, USA
| | - Guaciara M Santos
- Department of Earth Systems Sciences, University of California, Irvine Irvine, CA, USA
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55
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Pavillon N, Smith NI. Maximizing throughput in label-free microspectroscopy with hybrid Raman imaging. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:016007. [PMID: 25572258 DOI: 10.1117/1.jbo.20.1.016007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/02/2014] [Indexed: 06/04/2023]
Abstract
Raman spectroscopy is an optical method providing sample molecular composition, which can be analyzed (by point measurements) or spatially mapped by Raman imaging. These provide different information, signal-to-noise ratios, and require different acquisition times. Here, we quantitatively assess Raman spectral features and compare the two measurement methods by multivariate analysis. We also propose a hybrid method: scanning the beam through the sample but optically binning the signal at one location on the detector. This approach generates significantly more useful spectral signals in terms of peak visibility and statistical information. Additionally, by combination with a complementary imaging mode such as quantitative phase microscopy, hybrid imaging allows high throughput and robust spectral analysis while retaining sample spatial information. We demonstrate the improved ability to discriminate between cell lines when using hybrid scanning compared to typical point mode measurements, by quantitatively evaluating spectra taken from two macrophage-like cell lines. Hybrid scanning also provides better classification capability than the full Raman imaging mode, while providing higher signal-to-noise signals with shorter acquisition times. This hybrid imaging approach is suited for various applications including cytometry, cancer versus noncancer detection, and label-free discrimination of cell types or tissues.
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Affiliation(s)
- Nicolas Pavillon
- Osaka University, Immunology Frontier Research Center (IFReC), Biophotonics Laboratory, Suita, Osaka 565-0871, Japan
| | - Nicholas I Smith
- Osaka University, Immunology Frontier Research Center (IFReC), Biophotonics Laboratory, Suita, Osaka 565-0871, JapanbPRESTO, Japan Science and Technology Agency (JST), Chiyodaku, Tokyo 102-0076, Japan
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56
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Lis D, Cecchet F. Localized surface plasmon resonances in nanostructures to enhance nonlinear vibrational spectroscopies: towards an astonishing molecular sensitivity. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2014; 5:2275-92. [PMID: 25551056 PMCID: PMC4273228 DOI: 10.3762/bjnano.5.237] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/04/2014] [Indexed: 05/20/2023]
Abstract
Vibrational transitions contain some of the richest fingerprints of molecules and materials, providing considerable physicochemical information. Vibrational transitions can be characterized by different spectroscopies, and alternatively by several imaging techniques enabling to reach sub-microscopic spatial resolution. In a quest to always push forward the detection limit and to lower the number of needed vibrational oscillators to get a reliable signal or imaging contrast, surface plasmon resonances (SPR) are extensively used to increase the local field close to the oscillators. Another approach is based on maximizing the collective response of the excited vibrational oscillators through molecular coherence. Both features are often naturally combined in vibrational nonlinear optical techniques. In this frame, this paper reviews the main achievements of the two most common vibrational nonlinear optical spectroscopies, namely surface-enhanced sum-frequency generation (SE-SFG) and surface-enhanced coherent anti-Stokes Raman scattering (SE-CARS). They can be considered as the nonlinear counterpart and/or combination of the linear surface-enhanced infrared absorption (SEIRA) and surface-enhanced Raman scattering (SERS) techniques, respectively, which are themselves a branching of the conventional IR and spontaneous Raman spectroscopies. Compared to their linear equivalent, those nonlinear vibrational spectroscopies have proved to reach higher sensitivity down to the single molecule level, opening the way to astonishing perspectives for molecular analysis.
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Affiliation(s)
- Dan Lis
- Research Centre in Physics of Matter and Radiation (PMR), University of Namur (UNamur), 61 rue de Bruxelles, B-5000 Namur, Belgium
| | - Francesca Cecchet
- Research Centre in Physics of Matter and Radiation (PMR), University of Namur (UNamur), 61 rue de Bruxelles, B-5000 Namur, Belgium
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57
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Advanced experimental methods toward understanding biophysicochemical interactions of interfacial biomolecules by using sum frequency generation vibrational spectroscopy. Sci China Chem 2014. [DOI: 10.1007/s11426-014-5233-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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58
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Imaging without Fluorescence: Nonlinear Optical Microscopy for Quantitative Cellular Imaging. Anal Chem 2014; 86:8506-13. [DOI: 10.1021/ac5013706] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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59
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Alfonso-García A, Mittal R, Lee ES, Potma EO. Biological imaging with coherent Raman scattering microscopy: a tutorial. JOURNAL OF BIOMEDICAL OPTICS 2014; 19:71407. [PMID: 24615671 PMCID: PMC4019423 DOI: 10.1117/1.jbo.19.7.071407] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/27/2014] [Indexed: 05/05/2023]
Abstract
Coherent Raman scattering (CRS) microscopy is gaining acceptance as a valuable addition to the imaging toolset of biological researchers. Optimal use of this label-free imaging technique benefits from a basic understanding of the physical principles and technical merits of the CRS microscope. This tutorial offers qualitative explanations of the principles behind CRS microscopy and provides information about the applicability of this nonlinear optical imaging approach for biological research.
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Affiliation(s)
| | - Richa Mittal
- University of California, Beckman Laser Institute, Irvine, California 92697
| | - Eun Seong Lee
- Center for Nano-Bio Technology, Division of Convergence Technology, Korea Research Institute of Standards and Science, 1 Doryong-Dong, Yuseong-Gu, Daejeon 305-340, Republic of Korea
| | - Eric O. Potma
- University of California, Beckman Laser Institute, Irvine, California 92697
- Address all correspondence to: Eric O. Potma, E-mail:
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60
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El-Mashtoly SF, Niedieker D, Petersen D, Krauss SD, Freier E, Maghnouj A, Mosig A, Hahn S, Kötting C, Gerwert K. Automated identification of subcellular organelles by coherent anti-stokes Raman scattering. Biophys J 2014; 106:1910-20. [PMID: 24806923 PMCID: PMC4017266 DOI: 10.1016/j.bpj.2014.03.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/10/2014] [Accepted: 03/14/2014] [Indexed: 01/06/2023] Open
Abstract
Coherent anti-Stokes Raman scattering (CARS) is an emerging tool for label-free characterization of living cells. Here, unsupervised multivariate analysis of CARS datasets was used to visualize the subcellular compartments. In addition, a supervised learning algorithm based on the "random forest" ensemble learning method as a classifier, was trained with CARS spectra using immunofluorescence images as a reference. The supervised classifier was then used, to our knowledge for the first time, to automatically identify lipid droplets, nucleus, nucleoli, and endoplasmic reticulum in datasets that are not used for training. These four subcellular components were simultaneously and label-free monitored instead of using several fluorescent labels. These results open new avenues for label-free time-resolved investigation of subcellular components in different cells, especially cancer cells.
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Affiliation(s)
- Samir F El-Mashtoly
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Daniel Niedieker
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Dennis Petersen
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Sascha D Krauss
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Erik Freier
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Abdelouahid Maghnouj
- Department of Molecular GI-Oncology, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Axel Mosig
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Stephan Hahn
- Department of Molecular GI-Oncology, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Carsten Kötting
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Clinical Research Center, Ruhr-University Bochum, Bochum, Germany.
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61
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WINTERHALDER MJ, ZUMBUSCH A. Nonlinear optical microscopy with vibrational contrast. J Microsc 2014; 255:1-6. [DOI: 10.1111/jmi.12131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/24/2014] [Indexed: 02/01/2023]
Affiliation(s)
- M. J. WINTERHALDER
- Department of Chemistry; University of Konstanz; D-78457 Konstanz Germany
| | - A. ZUMBUSCH
- Department of Chemistry; University of Konstanz; D-78457 Konstanz Germany
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62
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Affiliation(s)
- Karen A. Antonio
- University of Notre Dame, Department of
Chemistry and Biochemistry, Notre
Dame, Indiana 46556, United States
| | - Zachary D. Schultz
- University of Notre Dame, Department of
Chemistry and Biochemistry, Notre
Dame, Indiana 46556, United States
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63
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Hu CR, Slipchenko MN, Wang P, Wang P, Lin JD, Simpson G, Hu B, Cheng JX. Stimulated Raman scattering imaging by continuous-wave laser excitation. OPTICS LETTERS 2013; 38:1479-81. [PMID: 23632524 PMCID: PMC3952503 DOI: 10.1364/ol.38.001479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate a low-cost-stimulated Raman scattering (SRS) microscope using continuous-wave (cw) lasers as excitation sources. A dual modulation scheme is used to remove the electronic background. The cw-SRS imaging of lipids in fatty liver is demonstrated by excitation of C─H stretch vibration.
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Affiliation(s)
- Chun-Rui Hu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of Science, Hefei 230027, China
| | - Mikhail N. Slipchenko
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ping Wang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Pu Wang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiandie D. Lin
- Life Science Institute, University of Michigan Medical Center, Ann Arbor, Michigan 48109, USA
| | - Garth Simpson
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Bing Hu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Science, University of Science and Technology of Science, Hefei 230027, China
| | - Ji-Xin Cheng
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA
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64
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Abstract
Multiphoton microscopy has enabled unprecedented dynamic exploration in living organisms. A significant challenge in biological research is the dynamic imaging of features deep within living organisms, which permits the real-time analysis of cellular structure and function. To make progress in our understanding of biological machinery, optical microscopes must be capable of rapid, targeted access deep within samples at high resolution. In this Review, we discuss the basic architecture of a multiphoton microscope capable of such analysis and summarize the state-of-the-art technologies for the quantitative imaging of biological phenomena.
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Affiliation(s)
- Erich E. Hoover
- Center for Microintegrated Optics for Advanced Bioimaging and Control, Colorado School of Mines, 1523 Illinois Street, Golden, Colorado 80401, USA
- Department of Physics, Colorado School of Mines, 1523 Illinois Street, Golden, Colorado 80401, USA
| | - Jeff A. Squier
- Center for Microintegrated Optics for Advanced Bioimaging and Control, Colorado School of Mines, 1523 Illinois Street, Golden, Colorado 80401, USA
- Department of Physics, Colorado School of Mines, 1523 Illinois Street, Golden, Colorado 80401, USA
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