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Zhu S, Li Y, Zhang F, Xiong C, Gao H, Yao Y, Qian W, Ding C, Chen S. Raman spectromics method for fast and label-free genotype screening. BIOMEDICAL OPTICS EXPRESS 2023; 14:3072-3085. [PMID: 37342689 PMCID: PMC10278603 DOI: 10.1364/boe.493524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
It is now understood that genes and their various mutations are associated with the onset and progression of diseases. However, routine genetic testing techniques are limited by their high cost, time consumption, susceptibility to contamination, complex operation, and data analysis difficulties, rendering them unsuitable for genotype screening in many cases. Therefore, there is an urgent need to develop a rapid, sensitive, user-friendly, and cost-effective method for genotype screening and analysis. In this study, we propose and investigate a Raman spectroscopic method for achieving fast and label-free genotype screening. The method was validated using spontaneous Raman measurements of wild-type Cryptococcus neoformans and its six mutants. An accurate identification of different genotypes was achieved by employing a one-dimensional convolutional neural network (1D-CNN), and significant correlations between metabolic changes and genotypic variations were revealed. Genotype-specific regions of interest were also localized and visualized using a gradient-weighted class activation mapping (Grad-CAM)-based spectral interpretable analysis method. Furthermore, the contribution of each metabolite to the final genotypic decision-making was quantified. The proposed Raman spectroscopic method demonstrated huge potential for fast and label-free genotype screening and analysis of conditioned pathogens.
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Affiliation(s)
- Shanshan Zhu
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
- Health Science Center, Ningbo University, Ningbo 315211, China
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350117, China
| | - Yanjian Li
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Fengdi Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
| | - Changchun Xiong
- College of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, China
| | - Han Gao
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
| | - Yudong Yao
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
| | - Wei Qian
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Shuo Chen
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Shenyang 110169, China
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Liu Z, Xue Y, Yang C, Li B, Zhang Y. Rapid identification and drug resistance screening of respiratory pathogens based on single-cell Raman spectroscopy. Front Microbiol 2023; 14:1065173. [PMID: 36778844 PMCID: PMC9909742 DOI: 10.3389/fmicb.2023.1065173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/03/2023] [Indexed: 01/27/2023] Open
Abstract
Respiratory infections rank fourth in the global economic burden of disease. Lower respiratory tract infections are the leading cause of death in low-income countries. The rapid identification of pathogens causing lower respiratory tract infections to help guide the use of antibiotics can reduce the mortality of patients with lower respiratory tract infections. Single-cell Raman spectroscopy is a "whole biological fingerprint" technique that can be used to identify microbial samples. It has the advantages of no marking and fast and non-destructive testing. In this study, single-cell Raman spectroscopy was used to collect spectral data of six respiratory tract pathogen isolates. The T-distributed stochastic neighbor embedding (t-SNE) isolation analysis algorithm was used to compare the differences between the six respiratory tract pathogens. The eXtreme Gradient Boosting (XGBoost) algorithm was used to establish a Raman phenotype database model. The classification accuracy of the isolated samples was 93-100%, and the classification accuracy of the clinical samples was more than 80%. Combined with heavy water labeling technology, the drug resistance of respiratory tract pathogens was determined. The study showed that single-cell Raman spectroscopy-D2O (SCRS-D2O) labeling could rapidly identify the drug resistance of respiratory tract pathogens within 2 h.
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Affiliation(s)
- Ziyu Liu
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,School of Life Science, Jilin University, Changchun, China
| | - Ying Xue
- HOOKE Instruments Ltd., Changchun, China
| | - Chun Yang
- Department of Laboratory Medicine, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bei Li
- HOOKE Instruments Ltd., Changchun, China,The State Key Lab of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences (CAS), Changchun, China
| | - Ying Zhang
- Department of Pediatric Respiratory, The First Hospital of Jilin University, Changchun, China,*Correspondence: Ying Zhang ✉
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Alunni Cardinali M, Morresi A, Fioretto D, Vivarelli L, Dallari D, Govoni M. Brillouin and Raman Micro-Spectroscopy: A Tool for Micro-Mechanical and Structural Characterization of Cortical and Trabecular Bone Tissues. MATERIALS 2021; 14:ma14226869. [PMID: 34832271 PMCID: PMC8618195 DOI: 10.3390/ma14226869] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/04/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023]
Abstract
Human bone is a specialized tissue with unique material properties, providing mechanical support and resistance to the skeleton and simultaneously assuring capability of adaptation and remodelling. Knowing the properties of such a structure down to the micro-scale is of utmost importance, not only for the design of effective biomimetic materials but also to be able to detect pathological alterations in material properties, such as micro-fractures or abnormal tissue remodelling. The Brillouin and Raman micro-spectroscopic (BRmS) approach has the potential to become a first-choice technique, as it is capable of simultaneously investigating samples’ mechanical and structural properties in a non-destructive and label-free way. Here, we perform a mapping of cortical and trabecular bone sections of a femoral epiphysis, demonstrating the capability of the technique for discovering the morpho-mechanics of cells, the extracellular matrix, and marrow constituents. Moreover, the interpretation of Brillouin and Raman spectra merged with an approach of data mining is used to compare the mechanical alterations in specimens excised from distinct anatomical areas and subjected to different sample processing. The results disclose in both cases specific alterations in the morphology and/or in the tissue chemical make-up, which strongly affects bone mechanical properties, providing a method potentially extendable to other important biomedical issues.
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Affiliation(s)
- Martina Alunni Cardinali
- Department of Physics and Geology, University of Perugia, Via A. Pascoli, I-06123 Perugia, Italy;
- Correspondence:
| | - Assunta Morresi
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, I-06123 Perugia, Italy;
| | - Daniele Fioretto
- Department of Physics and Geology, University of Perugia, Via A. Pascoli, I-06123 Perugia, Italy;
- CEMIN—Center of Excellence for Innovative Nanostructured Material, I-06123 Perugia, Italy
| | - Leonardo Vivarelli
- Reconstructive Orthopaedic Surgery and Innovative Techniques—Musculoskeletal Tissue Bank, IRCCS Istituto Ortopedico Rizzoli, Via G.C. Pupilli 1, 40136 Bologna, Italy; (L.V.); (D.D.); (M.G.)
| | - Dante Dallari
- Reconstructive Orthopaedic Surgery and Innovative Techniques—Musculoskeletal Tissue Bank, IRCCS Istituto Ortopedico Rizzoli, Via G.C. Pupilli 1, 40136 Bologna, Italy; (L.V.); (D.D.); (M.G.)
| | - Marco Govoni
- Reconstructive Orthopaedic Surgery and Innovative Techniques—Musculoskeletal Tissue Bank, IRCCS Istituto Ortopedico Rizzoli, Via G.C. Pupilli 1, 40136 Bologna, Italy; (L.V.); (D.D.); (M.G.)
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Resolving complex phenotypes with Raman spectroscopy and chemometrics. Curr Opin Biotechnol 2020; 66:277-282. [DOI: 10.1016/j.copbio.2020.09.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 12/30/2022]
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