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Li Y, Han Z, Nessler R, Yi Z, Hemmer P, Brick R, Sokolov AV, Scully MO. Optical multiband polarimetric modulation sensing for gender and species identification of flying native solitary pollinators. iScience 2023; 26:108265. [PMID: 38026192 PMCID: PMC10654587 DOI: 10.1016/j.isci.2023.108265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/13/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Native pollinators are crucial to local ecosystems but are under threat with the introduction of managed pollinators, e.g., honeybees (Apis mellifera). We explored the feasibility of employing the entomological lidar technique in native pollinator abundance studies. This study included individuals of both genders of three common solitary bee species, Osmia californica, Osmia lignaria, and Osmia ribifloris, native to North America. Properties including optical cross-section, degree of linear polarization, and wingbeat power spectra at all three wavelengths have been extracted from the insect signals collected by a compact stand-off sensing system. These properties are then used in the classification analysis. For species with temporal and spatial overlapping, the highest accuracies of our method exceed 96% (O. ribifloris & O. lignaria) and 93% (O. lignaria & O. californica). The benefit of employing the seasonal activity and foraging preference information in enhancing identification accuracy has been emphasized.
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Affiliation(s)
- Yiyun Li
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
| | - Zehua Han
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
| | - Reed Nessler
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
| | - Zhenhuan Yi
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
| | - Philip Hemmer
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
- Department of Electrical & Computer Engineering, Texas, A&M University, College Station, TX 77843–3127, USA
| | - Robert Brick
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
| | - Alexei V. Sokolov
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
- Department of Physics, Baylor University, Waco, TX 76798, USA
| | - Marlan O. Scully
- Institute for Quantum Science and Engineering, Department of Physics and Astronomy, Texas, A&M University, College Station, TX 77843–4242, USA
- Department of Physics, Baylor University, Waco, TX 76798, USA
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Shigeto S, Takeshita N. Raman Micro-spectroscopy and Imaging of Filamentous Fungi. Microbes Environ 2022; 37. [PMID: 35387945 PMCID: PMC10037093 DOI: 10.1264/jsme2.me22006] [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] [Indexed: 11/12/2022] Open
Abstract
Filamentous fungi grow by the elongation of tubular cells called hyphae and form mycelia through repeated hyphal tip growth and branching. Since hyphal growth is closely related to the ability to secrete large amounts of enzymes or invade host cells, a more detailed understanding and the control of its growth are important in fungal biotechnology, ecology, and pathogenesis. Previous studies using fluorescence imaging revealed many of the molecular mechanisms involved in hyphal growth. Raman microspectroscopy and imaging methods are now attracting increasing attention as powerful alternatives due to their high chemical specificity and label-free, non-destructive properties. Spatially resolved information on the relative abundance, structure, and chemical state of multiple intracellular components may be simultaneously obtained. Although Raman studies on filamentous fungi are still limited, this review introduces recent findings from Raman studies on filamentous fungi and discusses their potential use in the future.
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Affiliation(s)
- Shinsuke Shigeto
- Department of Chemistry, School of Science, Kwansei Gakuin University
| | - Norio Takeshita
- Microbiology Research Center for Sustainability (MiCS), Faculty of Life and Environmental Sciences, University of Tsukuba
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Korinth F, Shaik TA, Popp J, Krafft C. Assessment of shifted excitation Raman difference spectroscopy in highly fluorescent biological samples. Analyst 2021; 146:6760-6767. [PMID: 34704561 DOI: 10.1039/d1an01376a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Shifted excitation Raman difference spectroscopy (SERDS) can be used as an instrumental baseline correction technique to retrieve Raman bands in highly fluorescent samples. Genipin (GE) cross-linked equine pericardium (EP) was used as a model system since a blue pigment is formed upon cross-linking, which results in a strong fluorescent background in the Raman spectra. EP was cross-linked with 0.25% GE solution for 0.5 h, 2 h, 4 h, 6 h, 12 h, and 24 h, and compared with corresponding untreated EP. Raman spectra were collected with three different excitation wavelengths. For the assessment of the SERDS technique, the preprocessed SERDS spectra of two excitation wavelengths (784 nm-786 nm) were compared with the mathematical baseline-corrected Raman spectra at 785 nm excitation using extended multiplicative signal correction, rubberband, the sensitive nonlinear iterative peak and polynomial fitting algorithms. Whereas each baseline correction gave poor quality spectra beyond 6 h GE crosslinking with wave-like artefacts, the SERDS technique resulted in difference spectra, that gave superior reconstructed spectra with clear collagen and resonance enhanced GE pigment bands with lower standard deviation. Key for this progress was an advanced difference optimization approach that is described here. Furthermore, the results of the SERDS technique were independent of the intensity calibration because the system transfer response was compensated by calculating the difference spectrum. We conclude that this SERDS strategy can be transferred to Raman studies on biological and non-biological samples with a strong fluorescence background at 785 nm and also shorter excitation wavelengths which benefit from more intense scattering intensities and higher quantum efficiencies of CCD detectors.
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Affiliation(s)
- Florian Korinth
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany. .,Leibniz Institute for Astrophysics Potsdam and Member of Leibniz Research Alliance "Health Technologies", 14482 Potsdam, Germany
| | - Tanveer Ahmed Shaik
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany.
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany. .,Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, 07743 Jena, Germany
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology and Member of Leibniz Research Alliance "Health Technologies", 07745 Jena, Germany.
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Raman Characterization of Fungal DHN and DOPA Melanin Biosynthesis Pathways. J Fungi (Basel) 2021; 7:jof7100841. [PMID: 34682262 PMCID: PMC8540899 DOI: 10.3390/jof7100841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/16/2022] Open
Abstract
Fungal melanins represent a resource for important breakthroughs in industry and medicine, but the characterization of their composition, synthesis, and structure is not well understood. Raman spectroscopy is a powerful tool for the elucidation of molecular composition and structure. In this work, we characterize the Raman spectra of wild-type Aspergillus fumigatus and Cryptococcus neoformans and their melanin biosynthetic mutants and provide a rough “map” of the DHN (A. fumigatus) and DOPA (C. neoformans) melanin biosynthetic pathways. We compare this map to the Raman spectral data of Aspergillus nidulans wild-type and melanin biosynthetic mutants obtained from a previous study. We find that the fully polymerized A. nidulans melanin cannot be classified according to the DOPA pathway; nor can it be solely classified according to the DHN pathway, consistent with mutational analysis and chemical inhibition studies. Our approach points the way forward for an increased understanding of, and methodology for, investigating fungal melanins.
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Korinth F, Schmälzlin E, Stiebing C, Urrutia T, Micheva G, Sandin C, Müller A, Maiwald M, Sumpf B, Krafft C, Tränkle G, Roth MM, Popp J. Wide Field Spectral Imaging with Shifted Excitation Raman Difference Spectroscopy Using the Nod and Shuffle Technique. SENSORS (BASEL, SWITZERLAND) 2020; 20:E6723. [PMID: 33255459 PMCID: PMC7727830 DOI: 10.3390/s20236723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022]
Abstract
Wide field Raman imaging using the integral field spectroscopy approach was used as a fast, one shot imaging method for the simultaneous collection of all spectra composing a Raman image. For the suppression of autofluorescence and background signals such as room light, shifted excitation Raman difference spectroscopy (SERDS) was applied to remove background artifacts in Raman spectra. To reduce acquisition times in wide field SERDS imaging, we adapted the nod and shuffle technique from astrophysics and implemented it into a wide field SERDS imaging setup. In our adapted version, the nod corresponds to the change in excitation wavelength, whereas the shuffle corresponds to the shifting of charges up and down on a Charge-Coupled Device (CCD) chip synchronous to the change in excitation wavelength. We coupled this improved wide field SERDS imaging setup to diode lasers with 784.4/785.5 and 457.7/458.9 nm excitation and applied it to samples such as paracetamol and aspirin tablets, polystyrene and polymethyl methacrylate beads, as well as pork meat using multiple accumulations with acquisition times in the range of 50 to 200 ms. The results tackle two main challenges of SERDS imaging: gradual photobleaching changes the autofluorescence background, and multiple readouts of CCD detector prolong the acquisition time.
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Affiliation(s)
- Florian Korinth
- Leibniz Institute of Photonic Technology (Leibniz IPHT), Research Alliance “Health Technologies”, Albert-Einstein-Straße 9, 07743 Jena, Germany; (F.K.); (C.S.); (J.P.)
| | - Elmar Schmälzlin
- Leibniz Institute for Astrophysics Potsdam (AIP), Research Alliance “Health Technologies”, An der Sternwarte 16, 14482 Potsdam, Germany; (E.S.); (T.U.); (G.M.); (M.M.R.)
| | - Clara Stiebing
- Leibniz Institute of Photonic Technology (Leibniz IPHT), Research Alliance “Health Technologies”, Albert-Einstein-Straße 9, 07743 Jena, Germany; (F.K.); (C.S.); (J.P.)
| | - Tanya Urrutia
- Leibniz Institute for Astrophysics Potsdam (AIP), Research Alliance “Health Technologies”, An der Sternwarte 16, 14482 Potsdam, Germany; (E.S.); (T.U.); (G.M.); (M.M.R.)
| | - Genoveva Micheva
- Leibniz Institute for Astrophysics Potsdam (AIP), Research Alliance “Health Technologies”, An der Sternwarte 16, 14482 Potsdam, Germany; (E.S.); (T.U.); (G.M.); (M.M.R.)
| | - Christer Sandin
- Sandin Advanced Visualization, Tylögränd 14, 12156 Johanneshov, Sweden;
| | - André Müller
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Research Alliance “Health Technologies”, Gustav-Kirchhoff-Str. 4, 12489 Berlin, Germany; (A.M.); (M.M.); (B.S.); (G.T.)
| | - Martin Maiwald
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Research Alliance “Health Technologies”, Gustav-Kirchhoff-Str. 4, 12489 Berlin, Germany; (A.M.); (M.M.); (B.S.); (G.T.)
| | - Bernd Sumpf
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Research Alliance “Health Technologies”, Gustav-Kirchhoff-Str. 4, 12489 Berlin, Germany; (A.M.); (M.M.); (B.S.); (G.T.)
| | - Christoph Krafft
- Leibniz Institute of Photonic Technology (Leibniz IPHT), Research Alliance “Health Technologies”, Albert-Einstein-Straße 9, 07743 Jena, Germany; (F.K.); (C.S.); (J.P.)
| | - Günther Tränkle
- Ferdinand-Braun-Institut, Leibniz-Institut für Höchstfrequenztechnik, Research Alliance “Health Technologies”, Gustav-Kirchhoff-Str. 4, 12489 Berlin, Germany; (A.M.); (M.M.); (B.S.); (G.T.)
| | - Martin M. Roth
- Leibniz Institute for Astrophysics Potsdam (AIP), Research Alliance “Health Technologies”, An der Sternwarte 16, 14482 Potsdam, Germany; (E.S.); (T.U.); (G.M.); (M.M.R.)
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology (Leibniz IPHT), Research Alliance “Health Technologies”, Albert-Einstein-Straße 9, 07743 Jena, Germany; (F.K.); (C.S.); (J.P.)
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University Jena, Helmholtzweg 4, 07743 Jena, Germany
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Strycker BD, Han Z, Duan Z, Commer B, Wang K, Shaw BD, Sokolov AV, Scully MO. Identification of toxic mold species through Raman spectroscopy of fungal conidia. PLoS One 2020; 15:e0242361. [PMID: 33227000 PMCID: PMC7682877 DOI: 10.1371/journal.pone.0242361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/30/2020] [Indexed: 02/08/2023] Open
Abstract
We use a 785 nm shifted excitation Raman difference (SERDS) technique to measure the Raman spectra of the conidia of 10 mold species of especial toxicological, medical, and industrial importance, including Stachybotrys chartarum, Penicillium chrysogenum, Aspergillus fumigatus, Aspergillus flavus, Aspergillus oryzae, Aspergillus niger, and others. We find that both the pure Raman and fluorescence signals support the hypothesis that for an excitation wavelength of 785 nm the Raman signal originates from the melanin pigments bound within the cell wall of the conidium. In addition, the major features of the pure Raman spectra group into profiles that we hypothesize may be due to differences in the complex melanin biosynthesis pathways. We then combine the Raman spectral data with neural network models to predict species classification with an accuracy above 99%. Finally, the Raman spectral data of all species investigated is made freely available for download and use.
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Affiliation(s)
- Benjamin D. Strycker
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, United States of America
- Baylor University, Waco, Texas, United States of America
| | - Zehua Han
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Zheng Duan
- Center for Optical and Electromagnetic Research, South China Academy of Advanced, Optoelectronics, South China Normal University, Guangzhou, China
| | - Blake Commer
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Kai Wang
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Brian D. Shaw
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Alexei V. Sokolov
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, United States of America
- Baylor University, Waco, Texas, United States of America
| | - Marlan O. Scully
- Institute for Quantum Science and Engineering, Texas A&M University, College Station, Texas, United States of America
- Baylor University, Waco, Texas, United States of America
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