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Temperini ME, Polito R, Intze A, Gillibert R, Berkmann F, Baldassarre L, Giliberti V, Ortolani M. A mid-infrared laser microscope for the time-resolved study of light-induced protein conformational changes. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:064102. [PMID: 37862502 DOI: 10.1063/5.0136676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/26/2023] [Indexed: 10/22/2023]
Abstract
We have developed a confocal laser microscope operating in the mid-infrared range for the study of light-sensitive proteins, such as rhodopsins. The microscope features a co-aligned infrared and visible illumination path for the selective excitation and probing of proteins located in the IR focus only. An external-cavity tunable quantum cascade laser provides a wavelength tuning range (5.80-6.35 µm or 1570-1724 cm-1) suitable for studying protein conformational changes as a function of time delay after visible light excitation with a pulsed LED. Using cryogen-free detectors, the relative changes in the infrared absorption of rhodopsin thin films around 10-4 have been observed with a time resolution down to 30 ms. The measured full-width at half maximum of the Airy disk at λ = 6.08 µm in transmission mode with a confocal arrangement of apertures is 6.6 µm or 1.1λ. Dark-adapted sample replacement at the beginning of each photocycle is then enabled by exchanging the illuminated thin-film location with the microscope mapping stage synchronized to data acquisition and LED excitation and by averaging hundreds of time traces acquired in different nearby locations within a homogeneous film area. We demonstrate that this instrument provides crucial advantages for time-resolved IR studies of rhodopsin thin films with a slow photocycle. Time-resolved studies of inhomogeneous samples may also be possible with the presented instrument.
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Affiliation(s)
- Maria Eleonora Temperini
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Raffaella Polito
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Antonia Intze
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Raymond Gillibert
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Fritz Berkmann
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Leonetta Baldassarre
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
| | - Valeria Giliberti
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
| | - Michele Ortolani
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, Rome 00185, Italy
- Center for Life Nano & Neuro Science CL2NS, Istituto Italiano di Tecnologia, Viale Regina Elena 291, Rome 00161, Italy
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Rittel MF, Schmidt S, Weis CA, Birgin E, van Marwick B, Rädle M, Diehl SJ, Rahbari NN, Marx A, Hopf C. Spatial Omics Imaging of Fresh-Frozen Tissue and Routine FFPE Histopathology of a Single Cancer Needle Core Biopsy: A Freezing Device and Multimodal Workflow. Cancers (Basel) 2023; 15:2676. [PMID: 37345020 DOI: 10.3390/cancers15102676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/16/2023] [Accepted: 05/06/2023] [Indexed: 06/23/2023] Open
Abstract
The complex molecular alterations that underlie cancer pathophysiology are studied in depth with omics methods using bulk tissue extracts. For spatially resolved tissue diagnostics using needle biopsy cores, however, histopathological analysis using stained FFPE tissue and the immunohistochemistry (IHC) of a few marker proteins is currently the main clinical focus. Today, spatial omics imaging using MSI or IRI is an emerging diagnostic technology for the identification and classification of various cancer types. However, to conserve tissue-specific metabolomic states, fast, reliable, and precise methods for the preparation of fresh-frozen (FF) tissue sections are crucial. Such methods are often incompatible with clinical practice, since spatial metabolomics and the routine histopathology of needle biopsies currently require two biopsies for FF and FFPE sampling, respectively. Therefore, we developed a device and corresponding laboratory and computational workflows for the multimodal spatial omics analysis of fresh-frozen, longitudinally sectioned needle biopsies to accompany standard FFPE histopathology of the same biopsy core. As a proof-of-concept, we analyzed surgical human liver cancer specimens using IRI and MSI with precise co-registration and, following FFPE processing, by sequential clinical pathology analysis of the same biopsy core. This workflow allowed for a spatial comparison between different spectral profiles and alterations in tissue histology, as well as a direct comparison for histological diagnosis without the need for an extra biopsy.
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Affiliation(s)
- Miriam F Rittel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Cleo-Aron Weis
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Emrullah Birgin
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Björn van Marwick
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Matthias Rädle
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Steffen J Diehl
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Clinic of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Nuh N Rahbari
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Alexander Marx
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
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Wilk A, Drozdz A, Olbrich K, Janik-Olchawa N, Setkowicz Z, Chwiej J. Influence of measurement mode on the results of glioblastoma multiforme analysis with the FTIR microspectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 287:122086. [PMID: 36423418 DOI: 10.1016/j.saa.2022.122086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
Fourier Transform Infrared (FTIR) microspectroscopy is well known for its effectiveness in spectral and biochemical analyses of various materials. It enables to determine the sample biochemical composition by assigning detected frequencies, characteristic for functional groups of main biological macromolecules. In analysis of tissue sections one of two measurement modes, namely transmission and transflection, is usually applied. The first one has relatively straightforward geometry, hence it is considered to be more precise and accurate. However, IR-transparent media are very fragile and expensive. Transflection does not require expensive substrates, but is more prone to disruptive influence of Mie scattering as well as electric field standing wave effect. The excessive comparison of spectra' characteristics, obtained via both measurement modes, was performed in this paper. By the means of Mann-Whitney non-parametrical U test and PCA, the comparison of results obtained with both modes and assessment of usefulness of IR spectra obtained with transmission and transflection modes to differentiate between healthy and GBM-affected tissue, were performed. The main objective of the presented research is to compare the results of FTIR analysis of unfixed biological samples performed with transflection and transmission mode. In frame of the study we demonstrated the discrepancies between results of biochemical analysis performed based on data obtained with transmission and transflection. Such observation suggests that caution should be taken in drawing conclusions from the results obtained with transflection geometry, as its more prone to disruptive effects. Despite that, IR spectra developed with both modes allowed to distinguish GBM area from healthy tissue, which proves their diagnostic potential. Especially, application of the ME-EMSC correction of spectra before PCA enhances the performance of both methods to distinguish the analysed tissue areas.
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Affiliation(s)
- Aleksandra Wilk
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Agnieszka Drozdz
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland; Faculty of Biology and Biotechnology, Maria Curie-Sklodowska University, Akademicka 19, 20-033 Lublin, Poland.
| | - Karolina Olbrich
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Natalia Janik-Olchawa
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
| | - Zuzanna Setkowicz
- Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Joanna Chwiej
- Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Krakow, Poland
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Lehmann J, Schorz S, Rache A, Häußermann T, Rädle M, Reichwald J. Establishing Reliable Research Data Management by Integrating Measurement Devices Utilizing Intelligent Digital Twins. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23010468. [PMID: 36617065 PMCID: PMC9824845 DOI: 10.3390/s23010468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 06/01/2023]
Abstract
One of the main topics within research activities is the management of research data. Large amounts of data acquired by heterogeneous scientific devices, sensor systems, measuring equipment, and experimental setups have to be processed and ideally be managed by Findable, Accessible, Interoperable, and Reusable (FAIR) data management approaches in order to preserve their intrinsic value to researchers throughout the entire data lifecycle. The symbiosis of heterogeneous measuring devices, FAIR principles, and digital twin technologies is considered to be ideally suited to realize the foundation of reliable, sustainable, and open research data management. This paper contributes a novel architectural approach for gathering and managing research data aligned with the FAIR principles. A reference implementation as well as a subsequent proof of concept is given, leveraging the utilization of digital twins to overcome common data management issues at equipment-intense research institutes. To facilitate implementation, a top-level knowledge graph has been developed to convey metadata from research devices along with the produced data. In addition, a reactive digital twin implementation of a specific measurement device was devised to facilitate reconfigurability and minimized design effort.
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