1
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Leng H, Zhang Z, Chen C, Chen C. A class-imbalanced hybrid learning strategy based on Raman spectroscopy of serum samples for the diagnosis of hepatitis B, hepatitis A, and thyroid dysfunction. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 320:124581. [PMID: 38850829 DOI: 10.1016/j.saa.2024.124581] [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: 01/02/2024] [Revised: 05/19/2024] [Accepted: 05/30/2024] [Indexed: 06/10/2024]
Abstract
Computer-aided vibrational spectroscopy detection technology has achieved promising results in the field of early disease diagnosis. Yet limited by factors such as the number of actual samples and the cost of spectral acquisition in clinical medicine, the data available for model training are insufficient, and the amount of data varies greatly between different diseases, which constrain the performance optimization and enhancement of the diagnostic model. In this study, vibrational spectroscopy data of three common diseases are selected as research objects, and experimental research is conducted around the class imbalance situation that exists in medical data. When dealing with the challenge of class imbalance in medical vibrational spectroscopy research, it no longer relies on some kind of independent and single method, but considers the combined effect of multiple strategies. SVM, K-Nearest Neighbor (KNN), and Decision Tree (DT) are used as baseline comparison models on Raman spectroscopy medical datasets with different imbalance rates. The performance of the three strategies, Ensemble Learning, Feature Extraction, and Resampling, is verified on the class imbalance dataset by G-mean and AUC metrics, respectively. The results show that all the above three methods mitigate the negative impact caused by unbalanced learning. Based on this, we propose a hybrid ensemble classifier (HEC) that integrates resampling, feature extraction, and ensemble learning to verify the effectiveness of the hybrid learning strategy in solving the class imbalance problem. The G-mean and AUC values of the HEC method are 82.7 % and 83.12 % for the HBV dataset, is 2.02 % and 1.98 % higher than the optimal strategy; 83.62 % and 83.76 % for the HCV dataset, is 9.79 % and 8.47 % higher than the optimal strategy; while for the thyroid dysfunction dataset are 77.56 % and 77.85 %, is 6.92 % and 6.36 % higher than that of the optimal strategy, respectively. The experimental results show that the G-mean and AUC metrics of the HEC method are higher than those of the baseline classifier as well as the optimal combination using separate strategies. It can be seen that the HEC method can effectively counteract the unfavorable effects of imbalance learning and is expected to be applied to a wider range of imbalance scenarios.
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Affiliation(s)
- Hongyong Leng
- School of Computer Science & Technology, Beijing Institute of Technology, China; College of Software, Xinjiang University, Urumqi 830046, China
| | - Ziyang Zhang
- College of Software, Xinjiang University, Urumqi 830046, China
| | - Chen Chen
- College of Software, Xinjiang University, Urumqi 830046, China; Xinjiang Cloud Computing Application Laboratory, Karamay 834099, China
| | - Cheng Chen
- College of Software, Xinjiang University, Urumqi 830046, China.
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2
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Yu Q, Shen X, Yi L, Liang M, Li G, Guan Z, Wu X, Castel H, Hu B, Yin P, Zhang W. Fragment-Fusion Transformer: Deep Learning-Based Discretization Method for Continuous Single-Cell Raman Spectral Analysis. ACS Sens 2024. [PMID: 38934798 DOI: 10.1021/acssensors.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
Raman spectroscopy has become an important single-cell analysis tool for monitoring biochemical changes at the cellular level. However, Raman spectral data, typically presented as continuous data with high-dimensional characteristics, is distinct from discrete sequences, which limits the application of deep learning-based algorithms in data analysis due to the lack of discretization. Herein, a model called fragment-fusion transformer is proposed, which integrates the discrete fragmentation of continuous spectra based on their intrinsic characteristics with the extraction of intrafragment features and the fusion of interfragment features. The model integrates the intrinsic feature-based fragmentation of spectra with transformer, constructing the fragment transformer block for feature extraction within fragments. Interfragment information is combined through the pyramid design structure to improve the model's receptive field and fully exploit the spectral properties. During the pyramidal fusion process, the information gain of the final extracted features in the spectrum has been enhanced by a factor of 9.24 compared to the feature extraction stage within the fragment, and the information entropy has been enhanced by a factor of 13. The fragment-fusion transformer achieved a spectral recognition accuracy of 94.5%, which is 4% higher compared to the method without fragmentation and fusion processes on the test set of cell Raman spectroscopy identification experiments. In comparison to common spectral classification models such as KNN, SVM, logistic regression, and CNN, fragment-fusion transformer has achieved 4.4% higher accuracy than the best-performing CNN model. Fragment-fusion transformer method has the potential to serve as a general framework for discretization in the field of continuous spectral data analysis and as a research tool for analyzing the intrinsic information within spectra.
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Affiliation(s)
- Qiang Yu
- Hangzhou Institute of Technology, Xidian University, Hangzhou, Zhejiang 311200, China
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Xiaokun Shen
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - LangLang Yi
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Minghui Liang
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Guoqian Li
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Zhihui Guan
- School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
| | - Xiaoyao Wu
- School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan, Hebei 056038, China
| | - Helene Castel
- Institute of Research and Biomedical Innovation, University of Rouen Normandie, Mont-Saint-Aignan, 76821, France
| | - Bo Hu
- School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China
- School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan, Hebei 056038, China
- Xi'an Intelligent Precision Diagnosis and Treatment International Science and Technology Cooperation Base, Xi'an, Shaanxi 710126, China
| | - Pengju Yin
- School of Mathematics and Physics Science and Engineering, Hebei University of Engineering, Handan, Hebei 056038, China
| | - Wenbo Zhang
- School of Electronic Engineering, Xidian University, Xi'an, Shaanxi 710126, China
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3
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Jurowski K, Noga M, Kobylarz D, Niżnik Ł, Krośniak A. Multimodal Imaging Using Raman Spectroscopy and FTIR in a Single Analytical Instrument with a Microscope (Infrared Raman Microscopy AIRsight, Shimadzu): Opportunities and Applications. Int J Mol Sci 2024; 25:6884. [PMID: 38999996 PMCID: PMC11241415 DOI: 10.3390/ijms25136884] [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] [Received: 05/06/2024] [Revised: 06/04/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy are powerful analytical techniques widely used separately in different fields of study. Integrating these two powerful spectroscopic techniques into one device represents a groundbreaking advance in multimodal imaging. This new combination which merges the molecular vibrational information from Raman spectroscopy with the ability of FTIR to study polar bonds, creates a unique and complete analytical tool. Through a detailed examination of the microscope's operation and case studies, this article illustrates how this integrated analytical instrument can provide more thorough and accurate analysis than traditional methods, potentially revolutionising analytical sample characterisation. This article aims to present the features and possible uses of a unified instrument merging FTIR and Raman spectroscopy for multimodal imaging. It particularly focuses on the technological progress and collaborative benefits of these two spectroscopic techniques within the microscope system. By emphasising this approach's unique benefits and improved analytical capabilities, the authors aim to illustrate its applicability in diverse scientific and industrial sectors.
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Affiliation(s)
- Kamil Jurowski
- Laboratory of Innovative Toxicological Research and Analyzes, Institute of Medical Sciences, Medical College, Rzeszów University, Al. mjr. W. Kopisto 2a, 35-959 Rzeszów, Poland
- Department of Regulatory and Forensic Toxicology, Institute of Medical Expertises, ul. Aleksandrowska 67/93, 91-205 Łódź, Poland
| | - Maciej Noga
- Department of Regulatory and Forensic Toxicology, Institute of Medical Expertises, ul. Aleksandrowska 67/93, 91-205 Łódź, Poland
| | - Damian Kobylarz
- Department of Regulatory and Forensic Toxicology, Institute of Medical Expertises, ul. Aleksandrowska 67/93, 91-205 Łódź, Poland
| | - Łukasz Niżnik
- Department of Regulatory and Forensic Toxicology, Institute of Medical Expertises, ul. Aleksandrowska 67/93, 91-205 Łódź, Poland
| | - Alicja Krośniak
- Department of Regulatory and Forensic Toxicology, Institute of Medical Expertises, ul. Aleksandrowska 67/93, 91-205 Łódź, Poland
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4
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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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5
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Koyun OC, Keser RK, Şahin SO, Bulut D, Yorulmaz M, Yücesoy V, Töreyin BU. RamanFormer: A Transformer-Based Quantification Approach for Raman Mixture Components. ACS OMEGA 2024; 9:23241-23251. [PMID: 38854537 PMCID: PMC11154961 DOI: 10.1021/acsomega.3c09247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/03/2024] [Accepted: 05/10/2024] [Indexed: 06/11/2024]
Abstract
Raman spectroscopy is a noninvasive technique to identify materials by their unique molecular vibrational fingerprints. However, distinguishing and quantifying components in mixtures present challenges due to overlapping spectra, especially when components share similar features. This study presents "RamanFormer", a transformer-based model designed to enhance the analysis of Raman spectroscopy data. By effectively managing sequential data and integrating self-attention mechanisms, RamanFormer identifies and quantifies components in chemical mixtures with high precision, achieving a mean absolute error of 1.4% and a root mean squared error of 1.6%, significantly outperforming traditional methods such as least squares, MLP, VGG11, and ResNet50. Tested extensively on binary and ternary mixtures under varying conditions, including noise levels with a signal-to-noise ratio of up to 10 dB, RamanFormer proves to be a robust tool, improving the reliability of material identification and broadening the application of Raman spectroscopy in fields, such as material science, forensics, and biomedical diagnostics.
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Affiliation(s)
- Onur Can Koyun
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
| | - Reyhan Kevser Keser
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
| | | | - Damla Bulut
- ASELSAN
Inc, Yenimahalle, 06200 Ankara, Turkey
| | | | | | - Behçet Uğur Töreyin
- Signal
Processing for Computational Intelligence Research Group (SP4CING),
Informatics Institute, Istanbul Technical
University, 34469 Istanbul, Turkey
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6
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Pietruszewska M, Biesiada G, Czepiel J, Birczyńska-Zych M, Moskal P, Garlicki A, Wesełucha-Birczyńska A. Raman spectroscopy of lymphocytes from patients with the Epstein-Barr virus infection. Sci Rep 2024; 14:6417. [PMID: 38494496 PMCID: PMC10944829 DOI: 10.1038/s41598-024-56864-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/12/2024] [Indexed: 03/19/2024] Open
Abstract
In this study, Raman spectroscopy is applied to trace lymphocytes activation following contact with the Epstein-Barr virus (EBV) of the herpesvirus family. The biomarker of cell activation is found to be the 520 cm-1 band, indicating formation of immunoglobulins. The blood samples are obtained from patients diagnosed with infectious mononucleosis and treated at the University Hospital in Kraków. The lymphocytes' Raman spectra are collected using a mapping technique, exciting samples with a 514.5 nm line of Ar + laser. Measurements are performed on the 1st, 4th, 6th, 12th and 30th day of hospitalization, until the patient has recovered. The highest intensity of the immunoglobulin marker is observed on the 4th day of hospitalization, while the results of the blood count of patients show the greatest increase in the number of lymphocytes at the beginning of hospitalization. No activated lymphocytes were observed in the blood of healthy volunteers. Some information is provided by the evaluation of B-cell activation by estimating the activated areas in the cells, which are determined by the presence of the Ig marker. The 900 cm-1 band and band around 1450 cm-1 are also analyzed as markers of the presence of the latent membrane protein, LMP2A (and 2B), of the EBV viral protein. The anomalous degree of depolarization observed in B-cells in the course of EBV infection appears to be due to the influence of a virus protein, disrupting BCR signal transduction.
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Affiliation(s)
| | - Grażyna Biesiada
- Department of Infectious Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Jacek Czepiel
- Department of Infectious Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Malwina Birczyńska-Zych
- Department of Infectious Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
| | - Paulina Moskal
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387, Kraków, Poland
| | - Aleksander Garlicki
- Department of Infectious Diseases, Jagiellonian University, Medical College, Jakubowskiego 2, 30-688, Kraków, Poland
- The University Hospital in Kraków, Jakubowskiego 2, 30-688, Kraków, Poland
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7
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Zhang X, Fan A, Shu Z, Ma W, Zhang X. Surface-enhanced Raman database of 24 metabolites: Stable measurement of spectra, extraction and analysis of the main features. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123587. [PMID: 37918093 DOI: 10.1016/j.saa.2023.123587] [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: 04/06/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/04/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) has been used in Raman-based metabolomics to provide abundant molecular fingerprint information in situ with extremely high sensitivity, without damaging the sample. However, poor reproducibility, caused by the randomness of the adsorption sites, and the short-range effect of SERS have hindered the development of SERS in metabolomics, resulting in very few SERS reference databases for small-molecule metabolites. In this work, our previously proposed large laser spot-swift mapping SERS method was adopted for the measurement of 24 commercially available metabolite standards, to provide reproducible and reliable references for Raman-based metabolomics study. Among these 24 metabolites, 22 contained no Raman data in PubChem. Other than the SERS spectra data, we extracted and explained the molecular vibration information of these metabolites, and combined with the density functional theory (DFT) calculations, we provided a new possibility for the fast Raman recognition of small-molecule metabolites. Accordingly, a large laser spot-swift mapping SERS database of metabolites in human serum was initially established, which contained not only the original spectral data but also other detailed feature information regarding the Raman peaks. With continuous accumulation, this database could play a promising role in Raman-based metabolomics and other Raman-related research.
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Affiliation(s)
- Xiaoyu Zhang
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Aoran Fan
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Zixin Shu
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Weigang Ma
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China
| | - Xing Zhang
- Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Department of Engineering Mechanics, Tsinghua University, Beijing, 100084, China.
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8
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Martins C, Magalhães S, Almeida I, Neto V, Rebelo S, Nunes A. Metabolomics to Study Human Aging: A Review. Curr Mol Med 2024; 24:457-477. [PMID: 37026499 DOI: 10.2174/1566524023666230407123727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/17/2023] [Accepted: 02/17/2023] [Indexed: 04/08/2023]
Abstract
In the last years, with the increase in the average life expectancy, the world's population is progressively aging, which entails social, health and economic problems. In this sense, the need to better understand the physiology of the aging process becomes an urgent need. Since the study of aging in humans is challenging, cellular and animal models are widely used as alternatives. Omics, namely metabolomics, have emerged in the study of aging, with the aim of biomarker discovering, which may help to uncomplicate this complex process. This paper aims to summarize different models used for aging studies with their advantages and limitations. Also, this review gathers the published articles referring to biomarkers of aging already discovered using metabolomics approaches, comparing the results obtained in the different studies. Finally, the most frequently used senescence biomarkers are described, along with their importance in understanding aging.
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Affiliation(s)
- Claudia Martins
- Department of Medical Sciences, iBiMED: Institute of Biomedicine, University of Aveiro, Agra do Crasto, Aveiro 3810-193, Portugal
| | - Sandra Magalhães
- Department of Surgery and Physiology, Faculty of Medicine, UnIC@RISE, Cardiovascular Research & Development Centre, University of Porto, Alameda Prof. Hernâni Monteiro, Porto 4200-319, Portugal
| | - Idália Almeida
- Department of Medical Sciences, iBiMED: Institute of Biomedicine, University of Aveiro, Agra do Crasto, Aveiro 3810-193, Portugal
- CICECO: Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, Aveiro 3810-193, Portugal
| | - Vanessa Neto
- Department of Medical Sciences, iBiMED: Institute of Biomedicine, University of Aveiro, Agra do Crasto, Aveiro 3810-193, Portugal
| | - Sandra Rebelo
- Department of Medical Sciences, iBiMED: Institute of Biomedicine, University of Aveiro, Agra do Crasto, Aveiro 3810-193, Portugal
| | - Alexandra Nunes
- Department of Medical Sciences, iBiMED: Institute of Biomedicine, University of Aveiro, Agra do Crasto, Aveiro 3810-193, Portugal
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9
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Wang K, Chen J, Martiniuk J, Ma X, Li Q, Measday V, Lu X. Species identification and strain discrimination of fermentation yeasts Saccharomyces cerevisiae and Saccharomyces uvarum using Raman spectroscopy and convolutional neural networks. Appl Environ Microbiol 2023; 89:e0167323. [PMID: 38038459 PMCID: PMC10734496 DOI: 10.1128/aem.01673-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE The use of S. cerevisiae and S. uvarum yeast starter cultures is a common practice in the alcoholic beverage fermentation industry. As yeast strains from different or the same species have variable fermentation properties, rapid and reliable typing of yeast strains plays an important role in the final quality of the product. In this study, Raman spectroscopy combined with CNN achieved accurate identification of S. cerevisiae and S. uvarum isolates at both the species and strain levels in a rapid, non-destructive, and easy-to-operate manner. This approach can be utilized to test the identity of commercialized dry yeast products and to monitor the diversity of yeast strains during fermentation. It provides great benefits as a high-throughput screening method for agri-food and the alcoholic beverage fermentation industry. This proposed method has the potential to be a powerful tool to discriminate S. cerevisiae and S. uvarum strains in taxonomic, ecological studies and fermentation applications.
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Affiliation(s)
- Kaidi Wang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Jing Chen
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jay Martiniuk
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiangyun Ma
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Qifeng Li
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin, China
| | - Vivien Measday
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiaonan Lu
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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10
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Delrue C, Speeckaert R, Oyaert M, Kerre T, Rottey S, Coopman R, Huvenne W, De Bruyne S, Speeckaert MM. Infrared Spectroscopy: A New Frontier in Hematological Disease Diagnosis. Int J Mol Sci 2023; 24:17007. [PMID: 38069330 PMCID: PMC10707114 DOI: 10.3390/ijms242317007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Hematological diseases, due to their complex nature and diverse manifestations, pose significant diagnostic challenges in healthcare. The pressing need for early and accurate diagnosis has driven the exploration of novel diagnostic techniques. Infrared (IR) spectroscopy, renowned for its noninvasive, rapid, and cost-effective characteristics, has emerged as a promising adjunct in hematological diagnostics. This review delves into the transformative role of IR spectroscopy and highlights its applications in detecting and diagnosing various blood-related ailments. We discuss groundbreaking research findings and real-world applications while providing a balanced view of the potential and limitations of the technique. By integrating advanced technology with clinical needs, we offer insights into how IR spectroscopy may herald a new era of hematological disease diagnosis.
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Affiliation(s)
- Charlotte Delrue
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium;
| | | | - Matthijs Oyaert
- Department of Clinical Biology, Ghent University Hospital, 9000 Ghent, Belgium; (M.O.); (S.D.B.)
| | - Tessa Kerre
- Department of Hematology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Sylvie Rottey
- Department of Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Renaat Coopman
- Department of Oral, Maxillofacial and Plastic Surgery, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Wouter Huvenne
- Department of Head and Neck Surgery, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Sander De Bruyne
- Department of Clinical Biology, Ghent University Hospital, 9000 Ghent, Belgium; (M.O.); (S.D.B.)
| | - Marijn M. Speeckaert
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium;
- Research Foundation-Flanders (FWO), 1000 Brussels, Belgium
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11
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Donjuán-Loredo G, Espinosa-Tanguma R, Guevara E, Rodríguez-Aranda MDC, León-Bejarano F, Hernández-Vidales K, Ramírez-Elías M. Fatty Acid-Binding Proteins Identification during the Evolution of Metabolic Syndrome: A Raman Spectroscopy-Based Approach. Molecules 2023; 28:7472. [PMID: 38005194 PMCID: PMC10672738 DOI: 10.3390/molecules28227472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 11/26/2023] Open
Abstract
Excess fat in abdominal deposits is a risk factor for multiple conditions, including metabolic syndrome (MetS); lipid metabolism plays an essential role in these pathologies; fatty acid-binding proteins (FABPs) are dedicated to the cytosolic transport of fat. FABP4, whose primary source is adipose tissue, is released into the circulation, acting as an adipokine, while FABP5 also accompanies the adverse effects of MetS. FABP4 and 5 are potential biomarkers of MetS, but their behavior during syndrome evolution has not been determined. Raman spectroscopy has been applied as an alternative method to disease biomarker detection. In this work, we detected spectral changes related to FABP4 and 5 in the serum at different points of time, using an animal model of a high-fat diet-induced MetS. FABP4 and 5 spectral changes show a contribution during the evolution of MetS, which indicates alteration to a molecular level that predisposes to established MetS. These findings place FABPs as potential biomarkers of MetS and Raman spectroscopy as an alternative method for MetS assessment.
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Affiliation(s)
- Guadalupe Donjuán-Loredo
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Av. Venustiano Carranza 2405, Lomas los Filtros, San Luis Potosí 78210, Mexico
| | - Ricardo Espinosa-Tanguma
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, Av. Venustiano Carranza 2405, Lomas los Filtros, San Luis Potosí 78210, Mexico
| | - Edgar Guevara
- Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACyT), Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, San Luis Potosí 78210, Mexico
- Consejo Nacional de Humanidades, Ciencias y Tecnologías (CONAHCYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí 78210, Mexico
| | - María del Carmen Rodríguez-Aranda
- Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACyT), Universidad Autónoma de San Luis Potosí, Av. Sierra Leona 550, San Luis Potosí 78210, Mexico
| | - Fabiola León-Bejarano
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec 1570, Privadas del Pedregal, San Luis Potosí 78295, Mexico
| | - Karen Hernández-Vidales
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec 1570, Privadas del Pedregal, San Luis Potosí 78295, Mexico
| | - Miguel Ramírez-Elías
- Facultad de Ciencias, Universidad Autónoma de San Luis Potosí, Av. Chapultepec 1570, Privadas del Pedregal, San Luis Potosí 78295, Mexico
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Mattoli L, Pelucchini C, Fiordelli V, Burico M, Gianni M, Zambaldi I. Natural complex substances: From molecules to the molecular complexes. Analytical and technological advances for their definition and differentiation from the corresponding synthetic substances. PHYTOCHEMISTRY 2023; 215:113790. [PMID: 37487919 DOI: 10.1016/j.phytochem.2023.113790] [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: 03/28/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/26/2023]
Abstract
Natural complex substances (NCSs) are a heterogeneous family of substances that are notably used as ingredients in several products classified as food supplements, medical devices, cosmetics and traditional medicines, according to the correspondent regulatory framework. The compositions of NCSs vary widely and hundreds to thousands of compounds can be present at the same time. A key concept is that NCSs are much more than the simple sum of the compounds that constitute them, in fact some emerging phenomena are the result of the supramolecular interaction of the constituents of the system. Therefore, close attention should be paid to produce and characterize these systems. Today many natural compounds are produced by chemical synthesis and are intentionally added to NCSs, or to formulated natural products, to enhance their properties, lowering their production costs. Market analysis shows a tendency of people to use products made with NCSs and, currently, products made with ingredients of natural origin only are not conveniently distinguishable from those containing compounds of synthetic origin. Furthermore, the uncertainty of the current European regulatory framework does not allow consumers to correctly differentiate and identify products containing only ingredients of natural origin. The high demand for specific and effective NCSs and their high-cost offer on the market, create the conditions to economically motivated sophistications, characterized by the addition of a cheap material to a more expensive one, just to increase profit. This type of practice can concern both the addition of less valuable natural materials and the addition of pure artificial compounds with the same structure as those naturally present. In this scenario, it becomes essential for producers of natural products to have advanced analytical techniques to evaluate the effective naturalness of NCSs. In fact, synthetically obtained compounds are not identical to their naturally occurring counterparts, due to the isotopic composition or chirality, as well as the presence of different trace metabolites (since pure substances in nature do not exist). For this reason, in this review, the main analytical tests that can be performed to differentiate natural compounds from their synthetic counterparts will be highlighted and the main analytical technologies will be described. At the same time, the main fingerprint techniques useful for characterizing the complexity of the NCSs, also allowing their identification and quali-quantitative evaluation, will be described. Furthermore, NCSs can be produced through different manufacturing processes, not all of which are on the same level of quality. In this review the most suitable technologies for green processes that operate according to physical extraction principles will be presented, as according to the authors they are the ones that come closest to creating more life-cycle compatible NCSs and that are well suited to the European green deal, a strategy with the aim of transforming the EU into a sustainable and resource-efficient society by 2050.
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Affiliation(s)
- Luisa Mattoli
- Innovation & Medical Science, Aboca SpA, Sansepolcro, AR, Italy.
| | | | | | - Michela Burico
- Innovation & Medical Science, Aboca SpA, Sansepolcro, AR, Italy
| | - Mattia Gianni
- Innovation & Medical Science, Aboca SpA, Sansepolcro, AR, Italy
| | - Ilaria Zambaldi
- Innovation & Medical Science, Aboca SpA, Sansepolcro, AR, Italy
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13
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Guleken Z, Ceylan Z, Aday A, Bayrak AG, Hindilerden İY, Nalçacı M, Jakubczyk P, Jakubczyk D, Depciuch J. FTIR- based serum structure analysis in molecular diagnostics of essential thrombocythemia disease. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 245:112734. [PMID: 37295134 DOI: 10.1016/j.jphotobiol.2023.112734] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Essential thrombocythemia (ET) reflects the transformation of a multipotent hematopoietic stem cell, but its molecular pathogenesis remains obscure. Nevertheless, tyrosine kinase, especially Janus kinase 2 (JAK2), has been implicated in myeloproliferative disorders other than chronic myeloid leukaemia. FTIR analysis was performed on the blood serum of 86 patients and 45 healthy volunteers as control with FTIR spectra-based machine learning methods and chemometrics. Thus, the study aimed to determine biomolecular changes and separation of ET and healthy control groups illustration by applying chemometrics and ML techniques to spectral data. The FTIR-based results showed that in ET disease with JAK2 mutation, there are alterations in functional groups associated with lipids, proteins and nucleic acids significantly. Moreover, in ET patients the lower amount of proteins with simultaneously higher amount of lipids was noted in comparison with the control one. Furthermore, the SVM-DA model showed 100% accuracy in calibration sets in both spectral regions and 100.0% and 96.43% accuracy in prediction sets for the 800-1800 cm-1 and 2700-3000 cm-1 spectral regions, respectively. While changes in the dynamic spectra showed that CH2 bending, amide II and CO vibrations could be used as a spectroscopy marker of ET. Finally, it was found a positive correlation between FTIR peaks and first bone marrow fibrosis degree, as well as the absence of JAK2 V617F mutation. The findings of this study contribute to a better understanding of the molecular pathogenesis of ET and identifying biomolecular changes and may have implications for early diagnosis and treatment of this disease.
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Affiliation(s)
- Zozan Guleken
- Department of Physiology, Faculty of Medicine, Gaziantep, Islam, Science and Technology University, 27220, Gaziantep, Turkey.
| | - Zeynep Ceylan
- Samsun University, Faculty of Engineering, Department of Industrial Engineering, Turkey
| | - Aynur Aday
- Istanbul University, Faculty of Medicine, Department of Internal Medicine, Division of Medical Genetics, Turkey
| | - Ayşe Gül Bayrak
- Istanbul University, Faculty of Medicine, Department of Internal Medicine, Division of Medical Genetics, Turkey
| | - İpek Yönal Hindilerden
- Istanbul University Istanbul Faculty of Medicine, Department of Internal Medicine, Division of Hematology, Turkey
| | - Meliha Nalçacı
- Istanbul University Istanbul Faculty of Medicine, Department of Internal Medicine, Division of Hematology, Turkey
| | | | - Dorota Jakubczyk
- Faculty of Mathematics and Applied Physics, Rzeszow University of Technology, Powstancow Warszawy 12, PL-35959 Rzeszow, Poland
| | - Joanna Depciuch
- Institute of Nuclear Physics, PAS, 31342 Krakow, Poland; Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland
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Alkhuder K. Fourier-transform infrared spectroscopy: a universal optical sensing technique with auspicious application prospects in the diagnosis and management of autoimmune diseases. Photodiagnosis Photodyn Ther 2023; 42:103606. [PMID: 37187270 DOI: 10.1016/j.pdpdt.2023.103606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/17/2023]
Abstract
Autoimmune diseases (AIDs) are poorly understood clinical syndromes due to breakdown of immune tolerance towards specific types of self-antigens. They are generally associated with an inflammatory response mediated by lymphocytes T, autoantibodies or both. Ultimately, chronic inflammation culminates in tissue damages and clinical manifestations. AIDs affect 5% of the world population, and they represent the main cause of fatality in young to middle-aged females. In addition, the chronic nature of AIDs has a devastating impact on the patient's quality of life. It also places a heavy burden on the health care system. Establishing a rapid and accurate diagnosis is considered vital for an ideal medical management of these autoimmune disorders. However, for some AIDs, this task might be challenging. Vibrational spectroscopies, and more particularly Fourier-transform infrared (FTIR) spectroscopy, have emerged as universal analytical techniques with promising applications in the diagnosis of various types of malignancies and metabolic and infectious diseases. The high sensitivity of these optical sensing techniques and their minimal requirements for test reagents qualify them to be ideal analytical techniques. The aim of the current review is to explore the potential applications of FTIR spectroscopy in the diagnosis and management of most common AIDs. It also aims to demonstrate how this technique has contributed to deciphering the biochemical and physiopathological aspects of these chronic inflammatory diseases. The advantages that can be offered by this optical sensing technique over the traditional and gold standard methods used in the diagnosis of these autoimmune disorders have also been extensively discussed.
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15
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Alkhuder K. Raman Scattering-Based Optical Sensing Of Chronic Liver Diseases. Photodiagnosis Photodyn Ther 2023; 42:103505. [PMID: 36965755 DOI: 10.1016/j.pdpdt.2023.103505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/27/2023]
Abstract
Chronic liver diseases (CLDs) are a major public health problem. Despite the progress achieved in fighting against viral hepatitis, the emergence of non-alcoholic fatty liver disease might pose a serious challenge to the public's health in the coming decades. Medical management of CLDs represents a substantial burden on the public health infrastructures. The health care cost of these diseases is an additional burden that weighs heavily on the economies of developing countries. Effective management of CLDs requires the adoption of reliable and cost-effective screening and diagnosing methods to ensure early detection and accurate clinical assessment of these diseases. Vibrational spectroscopies have emerged as universal analytical methods with promising applications in various industrial and biomedical fields. These revolutionary analytical techniques rely on analyzing the interaction between a light beam and the test sample to generate a spectral fingerprint. This latter is defined by the analyte's chemical structure and the molecular vibrations of its functional groups. Raman spectroscopy and surface-enhanced Raman spectroscopy have been used in combination with various chemometric tests to diagnose a wide range of malignant, metabolic and infectious diseases. The aim of the current review is to cast light on the use of these optical sensing methods in the diagnosis of CLDs. The vast majority of research works that investigated the potential application of these spectroscopic techniques in screening and detecting CLDs were discussed here. The advantages and limitations of these modern analytical methods, as compared with the routine and gold standard diagnostic approaches, were also reviewed in details.
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Zhang X, Song X, Li W, Chen C, Wusiman M, Zhang L, Zhang J, Lu J, Lu C, Lv X. Rapid diagnosis of membranous nephropathy based on serum and urine Raman spectroscopy combined with deep learning methods. Sci Rep 2023; 13:3418. [PMID: 36854769 PMCID: PMC9974944 DOI: 10.1038/s41598-022-22204-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/11/2022] [Indexed: 03/02/2023] Open
Abstract
Membranous nephropathy is the main cause of nephrotic syndrome, which has an insidious onset and may progress to end-stage renal disease with a high mortality rate, such as renal failure and uremia. At present, the diagnosis of membranous nephropathy mainly relies on the clinical manifestations of patients and pathological examination of kidney biopsy, which are expensive, time-consuming, and have certain chance and other disadvantages. Therefore, there is an urgent need to find a rapid, accurate and non-invasive diagnostic technique for the diagnosis of membranous nephropathy. In this study, Raman spectra of serum and urine were combined with deep learning methods to diagnose membranous nephropathy. After baseline correction and smoothing of the data, Gaussian white noise of different decibels was added to the training set for data amplification, and the amplified data were imported into ResNet, AlexNet and GoogleNet models to obtain the evaluation results of the models for membranous nephropathy. The experimental results showed that the three deep learning models achieved an accuracy of 1 for the classification of serum data of patients with membranous nephropathy and control group, and the discrimination of urine data was above 0.85, among which AlexNet was the best classification model for both samples. The above experimental results illustrate the great potential of serum- and urine-based Raman spectroscopy combined with deep learning methods for rapid and accurate identification of patients with membranous nephropathy.
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Affiliation(s)
- Xueqin Zhang
- grid.410644.3People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830001 China
| | - Xue Song
- grid.410644.3People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830001 China
| | - Wenjing Li
- grid.413254.50000 0000 9544 7024College of Software, Xinjiang University, Urumqi, 830046 China
| | - Cheng Chen
- grid.413254.50000 0000 9544 7024College of Software, Xinjiang University, Urumqi, 830046 China
| | - Miriban Wusiman
- grid.13394.3c0000 0004 1799 3993Xinjiang Medical University, Urumqi, 830054 China
| | - Li Zhang
- grid.412631.3The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011 China
| | - Jiahui Zhang
- grid.13394.3c0000 0004 1799 3993Xinjiang Medical University, Urumqi, 830054 China
| | - Jinyu Lu
- grid.410644.3People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, 830001 China
| | - Chen Lu
- The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, China.
| | - Xiaoyi Lv
- College of Software, Xinjiang University, Urumqi, 830046, China.
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17
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Li C, Feng C, Xu R, Jiang B, Li L, He Y, Tu C, Li Z. The emerging applications and advancements of Raman spectroscopy in pediatric cancers. Front Oncol 2023; 13:1044177. [PMID: 36814817 PMCID: PMC9939836 DOI: 10.3389/fonc.2023.1044177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/18/2023] [Indexed: 02/09/2023] Open
Abstract
Although the survival rate of pediatric cancer has significantly improved, it is still an important cause of death among children. New technologies have been developed to improve the diagnosis, treatment, and prognosis of pediatric cancers. Raman spectroscopy (RS) is a non-destructive analytical technique that uses different frequencies of scattering light to characterize biological specimens. It can provide information on biological components, activities, and molecular structures. This review summarizes studies on the potential of RS in pediatric cancers. Currently, studies on the application of RS in pediatric cancers mainly focus on early diagnosis, prognosis prediction, and treatment improvement. The results of these studies showed high accuracy and specificity. In addition, the combination of RS and deep learning is discussed as a future application of RS in pediatric cancer. Studies applying RS in pediatric cancer illustrated good prospects. This review collected and analyzed the potential clinical applications of RS in pediatric cancers.
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Affiliation(s)
- Chenbei Li
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ruiling Xu
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Buchan Jiang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lan Li
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yu He
- Department of Radiology, Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chao Tu
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Chao Tu, ; Zhihong Li,
| | - Zhihong Li
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, China,Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Chao Tu, ; Zhihong Li,
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18
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de Almeida MP, Rodrigues C, Novais Â, Grosso F, Leopold N, Peixe L, Franco R, Pereira E. Silver Nanostar-Based SERS for the Discrimination of Clinically Relevant Acinetobacter baumannii and Klebsiella pneumoniae Species and Clones. BIOSENSORS 2023; 13:149. [PMID: 36831915 PMCID: PMC9953856 DOI: 10.3390/bios13020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
The development of rapid, reliable, and low-cost methods that enable discrimination among clinically relevant bacteria is crucial, with emphasis on those listed as WHO Global Priority 1 Critical Pathogens, such as carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant or ESBL-producing Klebsiella pneumoniae. To address this problem, we developed and validated a protocol of surface-enhanced Raman spectroscopy (SERS) with silver nanostars for the discrimination of A. baumannii and K. pneumoniae species, and their globally disseminated and clinically relevant antibiotic resistant clones. Isolates were characterized by mixing bacterial colonies with silver nanostars, followed by deposition on filter paper for SERS spectrum acquisition. Spectral data were processed with unsupervised and supervised multivariate data analysis methods, including principal component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), respectively. Our proposed SERS procedure using silver nanostars adsorbed to the bacteria, followed by multivariate data analysis, enabled differentiation between and within species. This pilot study demonstrates the potential of SERS for the rapid discrimination of clinically relevant A. baumannii and K. pneumoniae species and clones, displaying several advantages such as the ease of silver nanostars synthesis and the possible use of a handheld spectrometer, which makes this approach ideal for point-of-care applications.
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Affiliation(s)
- Miguel Peixoto de Almeida
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Carla Rodrigues
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 4TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU (IUCS-CESPU), 4585-116 Gandra, Portugal
| | - Filipa Grosso
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Nicolae Leopold
- Faculty of Physics, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ricardo Franco
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Química, School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Eulália Pereira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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Tian T, Zhang J, Xiong L, Yu H, Deng K, Liao X, Zhang F, Huang P, Zhang J, Chen Y. Evaluating Subtle Pathological Changes in Early Myocardial Ischemia Using Spectral Histopathology. Anal Chem 2022; 94:17112-17120. [PMID: 36442494 DOI: 10.1021/acs.analchem.2c03368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Early myocardial ischemia (EMI) is morphologically challenging, and the results from conventional histological staining may be subjective, imprecise, or even silent. The size of myocardial necrosis determines the acute and long-term mortality of EMI. The precise diagnosis of myocardial ischemia is critical for both clinical management and forensic investigation. Fourier transform infrared (FTIR) spectroscopic imaging is a highly sensitive tool for detecting protein conformations and imaging protein profiles. The aim of this study was to evaluate the application of FTIR imaging with multivariate analysis to detect biochemical changes in the protein conformation in the early phase of myocardial ischemia and to visually classify different disease states. The spectra and curve fitting results revealed that the total protein content decreased significantly in the EMI group and that the α-helix content of the secondary protein structure continuously decreased as ischemia progressed, while the β-sheet content increased. Differences in the control and EMI groups and perfused and ischemic myocardium were confirmed using principal component analysis and partial least squares discriminant analysis. Next, two support vector machine classifiers were effectively created. The accuracy, recall, and precision were 99.98, 99.96, and 100.00%, respectively, to differentiate the EMI group from the control group and 99.25, 98.95, and 99.54%, respectively, to differentiate perfused and ischemic myocardium. Ultimately, high EMI diagnostic accuracy was achieved with 100.00% recall and 100.00% precision, and ischemic myocardium diagnostic accuracy was achieved with 99.30% recall and 99.53% precision for the test set. This pilot study demonstrated that FTIR imaging is a powerful automated quantitative analysis tool to detect EMI without morphological changes and will improve diagnostic accuracy and patient prognosis.
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Affiliation(s)
- Tian Tian
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Jianhua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Ling Xiong
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China.,Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou 550004, P. R. China
| | - Haixing Yu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China.,College of Medicine & Forensics, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, P. R. China
| | - Kaifei Deng
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Xinbiao Liao
- Key Laboratory of Forensic Pathology, Ministry of Public Security, P. R. China, Guangzhou 510050, Guangdong, China
| | - Fu Zhang
- Key Laboratory of Forensic Pathology, Ministry of Public Security, P. R. China, Guangzhou 510050, Guangdong, China
| | - Ping Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Ji Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
| | - Yijiu Chen
- Department of Forensic Pathology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, P. R. China, Shanghai 200063, China
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20
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Villamanca JJ, Hermogino LJ, Ong KD, Paguia B, Abanilla L, Lim A, Angeles LM, Espiritu B, Isais M, Tomas RC, Albano PM. Predicting the Likelihood of Colorectal Cancer with Artificial Intelligence Tools Using Fourier Transform Infrared Signals Obtained from Tumor Samples. APPLIED SPECTROSCOPY 2022; 76:1412-1428. [PMID: 35821580 DOI: 10.1177/00037028221116083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The early and accurate detection of colorectal cancer (CRC) significantly affects its prognosis and clinical management. However, current standard diagnostic procedures for CRC often lack sensitivity and specificity since most rely on visual examination. Hence, there is a need to develop more accurate methods for its diagnosis. Support vector machine (SVM) and feedforward neural network (FNN) models were designed using the Fourier transform infrared (FT-IR) spectral data of several colorectal tissues that were unanimously identified as either benign or malignant by different unrelated pathologists. The set of samples in which the pathologists had discordant readings were then analyzed using the AI models described above. Between the SVM and NN models, the NN model was able to outperform the SVM model based on their prediction confidence scores. Using the spectral data of the concordant samples as training set, the FNN was able to predict the histologically diagnosed malignant tissues (n = 118) at 59.9-99.9% confidence (average = 93.5%). Of the 118 samples, 84 (71.18%) were classified with an above average confidence score, 34 (28.81%) classified below the average confidence score, and none was misclassified. Moreover, it was able to correctly identify the histologically confirmed benign samples (n = 83) at 51.5-99.7% confidence (average = 91.64%). Of the 83 samples, 60 (72.29%) were classified with an above average confidence score, 22 (26.51%) classified below the average confidence score, and only 1 sample (1.20%) was misclassified. The study provides additional proof of the ability of attenuated total reflection (ATR) FT-IR enhanced by AI tools to predict the likelihood of CRC without dependence on morphological changes in tissues.
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Affiliation(s)
- John Jerald Villamanca
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Lemuel John Hermogino
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Katherine Denise Ong
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Brian Paguia
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Lorenzo Abanilla
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
| | - Antonio Lim
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
| | - Lara Mae Angeles
- Department of Pathology, 596481University of Santo Tomas Hospital, Manila, Philippines
| | - Bernadette Espiritu
- Department of Pathology, 603332Bulacan Medical Center, Malolos City, Philippines
| | - Maura Isais
- Department of Pathology, 603332Bulacan Medical Center, Malolos City, Philippines
- The Graduate School, 595547University of Santo Tomas, Manila, Philippines
| | - Rock Christian Tomas
- Department of Electrical Engineering, 54729University of the Philippines Los Baños, Los Baños, Philippines
| | - Pia Marie Albano
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
- Research Center for the Natural and Applied Sciences, 564927University of Santo Tomas, Manila, Philippines
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Balytskyi Y, Bendesky J, Paul T, Hagen GM, McNear K. Raman Spectroscopy in Open-World Learning Settings Using the Objectosphere Approach. Anal Chem 2022; 94:15297-15306. [DOI: 10.1021/acs.analchem.2c02666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Yaroslav Balytskyi
- Department of Physics and Energy Science, University of Colorado, Colorado Springs, Colorado 80918, United States
- UCCS BioFrontiers Center, University of Colorado, Colorado Springs, Colorado 80918, United States
| | - Justin Bendesky
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Tristan Paul
- Department of Physics and Energy Science, University of Colorado, Colorado Springs, Colorado 80918, United States
- UCCS BioFrontiers Center, University of Colorado, Colorado Springs, Colorado 80918, United States
| | - Guy M. Hagen
- UCCS BioFrontiers Center, University of Colorado, Colorado Springs, Colorado 80918, United States
| | - Kelly McNear
- UCCS BioFrontiers Center, University of Colorado, Colorado Springs, Colorado 80918, United States
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22
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Mishra AK, Sudalaimuthuasari N, Hazzouri KM, Saeed EE, Shah I, Amiri KMA. Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques. Cells 2022; 11:3254. [PMID: 36291121 PMCID: PMC9600287 DOI: 10.3390/cells11203254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 10/21/2023] Open
Abstract
This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.
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Affiliation(s)
- Ajay Kumar Mishra
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Naganeeswaran Sudalaimuthuasari
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. Hazzouri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Esam Eldin Saeed
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Iltaf Shah
- Department of Chemistry (Biochemistry), College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Centre for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Jeon HJ, Kim HS, Chung E, Lee DY. Nanozyme-based colorimetric biosensor with a systemic quantification algorithm for noninvasive glucose monitoring. Theranostics 2022; 12:6308-6338. [PMID: 36168630 PMCID: PMC9475463 DOI: 10.7150/thno.72152] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/20/2022] [Indexed: 11/10/2022] Open
Abstract
Diabetes mellitus accompanies an abnormally high glucose level in the bloodstream. Early diagnosis and proper glycemic management of blood glucose are essential to prevent further progression and complications. Biosensor-based colorimetric detection has progressed and shown potential in portable and inexpensive daily assessment of glucose levels because of its simplicity, low-cost, and convenient operation without sophisticated instrumentation. Colorimetric glucose biosensors commonly use natural enzymes that recognize glucose and chromophores that detect enzymatic reaction products. However, many natural enzymes have inherent defects, limiting their extensive application. Recently, nanozyme-based colorimetric detection has drawn attention due to its merits including high sensitivity, stability under strict reaction conditions, flexible structural design with low-cost materials, and adjustable catalytic activities. This review discusses various nanozyme materials, colorimetric analytic methods and mechanisms, recent machine learning based analytic methods, quantification systems, applications and future directions for monitoring and managing diabetes.
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Affiliation(s)
- Hee-Jae Jeon
- Weldon School of Biomedical Engineering, Purdue University, Indiana 47906, USA
- Department of Mechanical and Biomedical Engineering, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyung Shik Kim
- Department of Bioengineering, College of Engineering, and BK FOUR Biopharmaceutical Innovation Leader for Education and Research Group, Hanyang University, Seoul 04763, Republic of Korea
| | - Euiheon Chung
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
- AI Graduate School, GIST, Gwangju 61005, Republic of Korea
- Research Center for Photon Science Technology, GIST, Gwangju 61005, Republic of Korea
| | - Dong Yun Lee
- Department of Bioengineering, College of Engineering, and BK FOUR Biopharmaceutical Innovation Leader for Education and Research Group, Hanyang University, Seoul 04763, Republic of Korea
- Institute of Nano Science and Technology (INST), Hanyang University, Seoul 04763, Republic of Korea
- Institute for Bioengineering and Biopharmaceutical Research (IBBR), Hanyang University, Seoul 04763, Republic of Korea
- Elixir Pharmatech Inc., Seoul 07463, Republic of Korea
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24
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Progress and Challenges of Point-of-Need Photonic Biosensors for the Diagnosis of COVID-19 Infections and Immunity. BIOSENSORS 2022; 12:bios12090678. [PMID: 36140063 PMCID: PMC9496547 DOI: 10.3390/bios12090678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/13/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022]
Abstract
The new coronavirus disease, COVID-19, caused by SARS-CoV-2, continues to affect the world and after more than two years of the pandemic, approximately half a billion people are reported to have been infected. Due to its high contagiousness, our life has changed dramatically, with consequences that remain to be seen. To prevent the transmission of the virus, it is crucial to diagnose COVID-19 accurately, such that the infected cases can be rapidly identified and managed. Currently, the gold standard of testing is polymerase chain reaction (PCR), which provides the highest accuracy. However, the reliance on centralized rapid testing modalities throughout the COVID-19 pandemic has made access to timely diagnosis inconsistent and inefficient. Recent advancements in photonic biosensors with respect to cost-effectiveness, analytical performance, and portability have shown the potential for such platforms to enable the delivery of preventative and diagnostic care beyond clinics and into point-of-need (PON) settings. Herein, we review photonic technologies that have become commercially relevant throughout the COVID-19 pandemic, as well as emerging research in the field of photonic biosensors, shedding light on prospective technologies for responding to future health outbreaks. Therefore, in this article, we provide a review of recent progress and challenges of photonic biosensors that are developed for the testing of COVID-19, consisting of their working fundamentals and implementation for COVID-19 testing in practice with emphasis on the challenges that are faced in different development stages towards commercialization. In addition, we also present the characteristics of a biosensor both from technical and clinical perspectives. We present an estimate of the impact of testing on disease burden (in terms of Disability-Adjusted Life Years (DALYs), Quality Adjusted Life Years (QALYs), and Quality-Adjusted Life Days (QALDs)) and how improvements in cost can lower the economic impact and lead to reduced or averted DALYs. While COVID19 is the main focus of these technologies, similar concepts and approaches can be used and developed for future outbreaks of other infectious diseases.
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25
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Haldavnekar R, Venkatakrishnan K, Tan B. Cancer Stem Cell Derived Extracellular Vesicles with Self-Functionalized 3D Nanosensor for Real-Time Cancer Diagnosis: Eliminating the Roadblocks in Liquid Biopsy. ACS NANO 2022; 16:12226-12243. [PMID: 35968931 DOI: 10.1021/acsnano.2c02971] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Liquid biopsy for determining the presence of cancer and the underlying tissue of origin is crucial to overcome the limitations of existing tissue biopsy and imaging-based techniques by capturing critical information from the dynamic tumor heterogeneity. A newly emerging liquid biopsy with extracellular vesicles (EVs) is gaining momentum, but its clinical relevance is in question due to the biological and technical challenges posed by existing technologies. The biological barriers of existing technologies include the inability to generate fundamental details of molecular structure, chemical composition as well as functional variations in EVs by gathering simultaneous information on multiple intra-EV molecules, unavailability of holistic qualitative analysis, in addition to the inability to identify tissue of origin. Technological barriers include reliance on EV isolation with a few labeled biomarkers, resulting in the inability to generate comprehensive information on the disease. A more favorable approach would be to generate holistic information on the disease without the use of labels. Such a marker-free diagnosis is impossible with the existing liquid biopsy due to the unavailability clinically validated cancer stem cells (CSC)-specific markers and dependence of existing technologies on EV isolation, undermining the clinical relevance of EV-based liquid biopsy. Here, CSC EVs were employed as an independent liquid biopsy modality. We hypothesize that tracking the signals of CSCs in peripheral blood with CSC EVs will provide a reliable solution for accurate cancer diagnosis, as CSC are the originators of tumor contributing to tumor heterogeneity. We report nanoengineered 3D sensors of extremely small nano-scaled probes self-functionalized for SERS, enabling integrative molecular and functional profiling of otherwise undetectable CSC EVs. A substantially enhanced SERS and ultralow limit of detection (10 EVs per 10 μL) were achieved. This was attributed to the efficient probe-EV interaction due to the 3D networks of nanoprobes, ensuring simultaneous detection of multiple EV signals. We experimentally demonstrate the crucial role of CSC EVs in cancer diagnosis. We then completed a pilot validation of this modality for cancer detection as well as for identification of the tissue of origin. An artificial neural network distinguished cancer from noncancer with 100% sensitivity and 100% specificity for three hard to detect cancers (breast, lung, and colorectal cancer). Binary classification to distinguish one tissue of origin against all other achieved 100% accuracy, while simultaneous identification of all three tissues of origin with multiclass classification achieved up to 79% accuracy. This noninvasive tool may complement existing cancer diagnostics, treatment monitoring as well as longitudinal disease monitoring by validation with a large cohort of clinical samples.
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Affiliation(s)
- Rupa Haldavnekar
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Ryerson University and St. Michael's Hospital, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
- Nano-Bio Interface Facility, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, Ontario M5B 1W8, Canada
- Nanocharacterization Laboratory, Faculty of Engineering and Architectural Sciences, Ryerson University, 350 Victoria Street, Toronto, Ontario M5B 2K3, Canada
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26
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Effects of the coupling of dielectric spherical particles on signatures in infrared microspectroscopy. Sci Rep 2022; 12:13327. [PMID: 35922455 PMCID: PMC9349280 DOI: 10.1038/s41598-022-16857-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/18/2022] [Indexed: 11/08/2022] Open
Abstract
Infrared microspectroscopy is a powerful tool in the analysis of biological samples. However, strong electromagnetic scattering may occur since the wavelength of the incident radiation and the samples may be of comparable size. Based on the Mie theory of single spheres, correction algorithms have been developed to retrieve pure absorbance spectra. Studies of the scattering characteristics of samples of different types, obtained by microspectroscopy, have been performed. However, the detailed, microscopic effects of the coupling of the samples on signatures in spectra, obtained by infrared microspectroscopy, are still not clear. The aim of this paper is to investigate how the coupling of spherical samples influences the spectra. Applying the surface integral equation (SIE) method, we simulate small dielectric spheres, arranged as double-spheres or small arrays of spheres. We find that the coupling of the spheres hardly influences the broad oscillations observed in infrared spectra (the Mie wiggles) unless the radii of the spheres are different or the angle between the direction of the incident radiation and the normal of the plane where the spheres are located is large. Sharp resonance features in the spectra (the Mie ripples) are affected by the coupling of the spheres and this effect depends on the polarization of the incident wave. Experiments are performed to verify our conclusions.
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27
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Rocchetti MT, Spadaccino F, Catalano V, Zaza G, Stallone G, Fiocco D, Netti GS, Ranieri E. Metabolic Fingerprinting of Fabry Disease: Diagnostic and Prognostic Aspects. Metabolites 2022; 12:metabo12080703. [PMID: 36005574 PMCID: PMC9415061 DOI: 10.3390/metabo12080703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022] Open
Abstract
Fabry disease (FD) is an X-linked lysosomal disease due to a deficiency in the activity of the lysosomal-galactosidase A (GalA), a key enzyme in the glycosphingolipid degradation pathway. FD is a complex disease with a poor genotype–phenotype correlation. In the early stages, FD could involve the peripheral nervous system (acroparesthesias and dysautonomia) and the ski (angiokeratoma), but later kidney, heart or central nervous system impairment may significantly decrease life expectancy. The advent of omics technologies offers the possibility of a global, integrated and systemic approach well-suited for the exploration of this complex disease. In this narrative review, we will focus on the main metabolomic studies, which have underscored the importance of detecting biomarkers for a diagnostic and prognostic purpose in FD. These investigations are potentially useful to explain the wide clinical, biochemical and molecular heterogeneity found in FD patients. Moreover, the quantitative mass spectrometry methods developed to evaluate concentrations of these biomarkers in urine and plasma will be described. Finally, the complex metabolic biomarker profile depicted in FD patients will be reported, which varies according to gender, types of mutations, and therapeutic treatment.
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Affiliation(s)
- Maria Teresa Rocchetti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (D.F.)
| | - Federica Spadaccino
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (V.C.); (E.R.)
| | - Valeria Catalano
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (V.C.); (E.R.)
| | - Gianluigi Zaza
- Unit of Nephology, Dialysis and Transplantation, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.Z.); (G.S.)
| | - Giovanni Stallone
- Unit of Nephology, Dialysis and Transplantation, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (G.Z.); (G.S.)
| | - Daniela Fiocco
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy; (M.T.R.); (D.F.)
| | - Giuseppe Stefano Netti
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (V.C.); (E.R.)
- Correspondence: ; Tel.: +39-0881-732619
| | - Elena Ranieri
- Unit of Clinical Pathology, Center for Molecular Medicine, Department of Medical and Surgical Sciences, University of Foggia, 71122 Foggia, Italy; (F.S.); (V.C.); (E.R.)
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28
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A Novel Method for Detecting Duchenne Muscular Dystrophy in Blood Serum of mdx Mice. Genes (Basel) 2022; 13:genes13081342. [PMID: 36011258 PMCID: PMC9407179 DOI: 10.3390/genes13081342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common form of muscular dystrophy, typically affecting males in infancy. The disease causes progressive weakness and atrophy of skeletal muscles, with approximately 20,000 new cases diagnosed yearly. Currently, methods for diagnosing DMD are invasive, laborious, and unable to make accurate early detections. While there is no cure for DMD, there are limited treatments available for managing symptoms. As such, there is a crucial unmet need to develop a simple and non-invasive method for accurately detecting DMD as early as possible. Raman spectroscopy with chemometric analysis is shown to have the potential to fill this diagnostic need.
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29
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Li D, Aubertin K, Onidas D, Nizard P, Félidj N, Gazeau F, Mangeney C, Luo Y. Recent advances in non-plasmonic surface-enhanced Raman spectroscopy nanostructures for biomedical applications. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1795. [PMID: 35362261 DOI: 10.1002/wnan.1795] [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: 12/29/2021] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is an emerging powerful vibrational technique offering unprecedented opportunities in biomedical science for the sensitive detection of biomarkers and the imaging and tracking of biological samples. Conventional SERS detection is based on the use of plasmonic substrates (e.g., Au and Ag nanostructures), which exhibit very high enhancement factors (EF = 1010 -1011 ) but suffers from serious limitations, including light-induced local heating effect due to ohmic loss and expensive price. These drawbacks may limit detection accuracy and large-scaled practical applications. In this review, we focus on alternative approaches based on plasmon-free SERS detection on low-cost nanostructures, such as carbons, oxides, chalcogenides, polymers, silicons, and so forth. The mechanism of non-plasmonic SERS detection has been attributed to interfacial charge transfer between the substrate and the adsorbed molecules, with no photothermal side-effects but usually less EF compared with plasmonic nanostructures. The strategies to improve Raman signal detection, through the tailoring of substrate composition, structure, and surface chemistry, is reviewed and discussed. The biomedical applications, for example, SERS cell characterization, biosensing, and bioimaging are also presented, highlighting the importance of substrate surface functionalization to achieve sensitive, accurate analysis, and excellent biocompatibility. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing Diagnostic Tools > In Vivo Nanodiagnostics and Imaging.
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Affiliation(s)
- Da Li
- LCBPT, CNRS UMR 8601, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Kelly Aubertin
- MSC, CNRS UMR 7057, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Delphine Onidas
- LCBPT, CNRS UMR 8601, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Philippe Nizard
- LCBPT, CNRS UMR 8601, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Nordin Félidj
- ITODYS, CNRS UMR 7086, Université Paris Cité, 15, rue Jean Antoine de Baïf, Paris, France
| | - Florence Gazeau
- MSC, CNRS UMR 7057, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Claire Mangeney
- LCBPT, CNRS UMR 8601, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
| | - Yun Luo
- LCBPT, CNRS UMR 8601, Université Paris Cité, 45, rue des Saints-Pères, Paris, France
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30
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Cameron JM, Rinaldi C, Rutherford SH, Sala A, G Theakstone A, Baker MJ. Clinical Spectroscopy: Lost in Translation? APPLIED SPECTROSCOPY 2022; 76:393-415. [PMID: 34041957 DOI: 10.1177/00037028211021846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This Focal Point Review paper discusses the developments of biomedical Raman and infrared spectroscopy, and the recent strive towards these technologies being regarded as reliable clinical tools. The promise of vibrational spectroscopy in the field of biomedical science, alongside the development of computational methods for spectral analysis, has driven a plethora of proof-of-concept studies which convey the potential of various spectroscopic approaches. Here we report a brief review of the literature published over the past few decades, with a focus on the current technical, clinical, and economic barriers to translation, namely the limitations of many of the early studies, and the lack of understanding of clinical pathways, health technology assessments, regulatory approval, clinical feasibility, and funding applications. The field of biomedical vibrational spectroscopy must acknowledge and overcome these hurdles in order to achieve clinical efficacy. Current prospects have been overviewed with comment on the advised future direction of spectroscopic technologies, with the aspiration that many of these innovative approaches can ultimately reach the frontier of medical diagnostics and many clinical applications.
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Affiliation(s)
| | - Christopher Rinaldi
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Alexandra Sala
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Ashton G Theakstone
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
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31
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Theakstone A, Brennan PM, Ashton K, Czeiter E, Jenkinson M, Syed K, Reed M, Baker M. Vibrational spectroscopy for the triage of traumatic brain injury CT priority and hospital admissions. J Neurotrauma 2022; 39:773-783. [PMID: 35236121 PMCID: PMC9225408 DOI: 10.1089/neu.2021.0410] [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] [Indexed: 11/12/2022] Open
Abstract
Computed Tomogram (CT) brain imaging is routinely used to support clinical decision-making in patients with traumatic brain injury (TBI). However, only 7% of scans demonstrate evidence of TBI. The other 93% of scans contribute a significant cost to the healthcare system and a radiation risk to patients. There may be better strategies to identify which patients, particularly those with mild TBI, are at risk of deterioration and require hospital admission. We introduce a blood serum liquid biopsy that utilises attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy with machine learning algorithms as a decision-making tool to identify which mild TBI patients will most benefit from CT brain imaging. Serum samples were obtained from (n=298) patients who had acquired a TBI and were enrolled in CENTER-TBI, and from asymptomatic control patients (n=87). Injury patients (all severities) were stratified against non-injury controls. The mild TBI cohort was further examined by stratifying those who had at least one CT abnormality against those who had no CT abnormalities. The test performed exceptionally well in classifications of mild injury patients versus non-injury controls (sensitivity = 96.4% and specificity = 98.0%) and also provided a sensitivity of 80.2% when stratifying mild patients with at least one CT abnormality against those without. The results provided illustrate the test ability to identify 4 out of every 5 CT abnormalities and shows great promise to be introduced as a triage tool for CT priority in mild TBI patients.
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Affiliation(s)
- Ashton Theakstone
- University of Strathclyde, 3527, 99 George Street, Glasgow, United Kingdom of Great Britain and Northern Ireland, G1 1RD;
| | - Paul M Brennan
- The University of Edinburgh Centre for Clinical Brain Sciences, 439257, Translational Neurosurgery, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Katherine Ashton
- Lancashire Teaching Hospitals NHS Foundation Trust, 6724, Neuropathology, Preston, Lancashire, United Kingdom of Great Britain and Northern Ireland;
| | - Endre Czeiter
- University of Pecs Medical School, 37657, Department of Neurosurgery, Pecs, Hungary.,University of Pecs, 37656, Neurotrauma Research Group, Szentágothai Research Centre, Pecs, Hungary.,University of Pecs, 37656, MTA-PTE Clinical Neuroscience MR Research Group, Pecs, Hungary;
| | - Michael Jenkinson
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland.,University of Liverpool, 4591, Department of Pharmacology & Therapeutics, Liverpool, Merseyside, United Kingdom of Great Britain and Northern Ireland;
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Reed
- Royal Infirmary of Edinburgh, 59843, Department of Emergency Medicine, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Baker
- Dxcover Limited, Glasgow, United Kingdom of Great Britain and Northern Ireland;
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32
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Nejdl L, Havlikova M, Mravec F, Vaculovic T, Faltusova V, Pavelicova K, Baron M, Kumsta M, Ondrousek V, Adam V, Vaculovicova M. UV-Induced fingerprint spectroscopy. Food Chem 2022; 368:130499. [PMID: 34496333 DOI: 10.1016/j.foodchem.2021.130499] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/22/2021] [Accepted: 06/27/2021] [Indexed: 01/04/2023]
Abstract
Here, we present the potential analytical applications of photochemistry in combination with fluorescence fingerprinting. Our approach analyzes the fluorescence of samples after ultraviolet light (UV) treatment. Especially in presence of metal ions and thiol-containing compounds, the fluorescence behavior changes considerably. The UV-induced reactions (changes) are unique to a given sample composition, resulting in distinct patterns or fingerprints (typically in the 230-600 nm spectral region). This method works without the need for additional chemicals or fluorescent probes, only suitable diluent must be used. The proposed method (UV fingerprinting) suggests the option of recognizing various types of pharmaceuticals, beverages (juices and wines), and other samples within only a few minutes. In some studied samples (e.g. pharmaceuticals), significant changes in fluorescence characteristics (mainly fluorescence intensity) were observed. We believe that the fingerprinting technique can provide an innovative solution for analytical detection.
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Affiliation(s)
- Lukas Nejdl
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ 613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic
| | - Martina Havlikova
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - Filip Mravec
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Purkynova 118, 612 00 Brno, Czech Republic
| | - Tomas Vaculovic
- Department of Chemistry, Masaryk University, Faculty of Science, Kamenice 5, 62500 Brno, Czech Republic
| | - Veronika Faltusova
- Department of Chemistry, Masaryk University, Faculty of Science, Kamenice 5, 62500 Brno, Czech Republic
| | - Kristyna Pavelicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ 613 00 Brno, Czech Republic
| | - Mojmir Baron
- Department of Viticulture and Enology, Mendel University in Brno, Lednice, Czech Republic
| | - Michal Kumsta
- Department of Viticulture and Enology, Mendel University in Brno, Lednice, Czech Republic
| | - Vit Ondrousek
- Department of Informatics, Mendel University in Brno, Zemedelska 1, CZ 613 00 Brno, Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ 613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic
| | - Marketa Vaculovicova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ 613 00 Brno, Czech Republic; Central European Institute of Technology, Brno University of Technology, Purkynova 123, CZ-612 00 Brno, Czech Republic.
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Acemi A. Monitoring the effects of chitosan on the profile of certain cell wall and membrane biomolecules in the leaves of Eruca vesicaria ssp. sativa through FT-IR spectroscopy. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 173:25-32. [PMID: 35092928 DOI: 10.1016/j.plaphy.2022.01.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 12/27/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The present study aimed to investigate the effects of chitosan at different molecular weights on the biomolecule profile of cell walls and membranes in Eruca vesicaria ssp. sativa leaves through FT-IR spectroscopy. It was demonstrated that the chitosan treatments could increase membrane destabilization through the elevation of lipid peroxidation and/or membrane fluidity. However, 10 kDa chitosan at 5 mg L-1 treatment was estimated to increase membrane lipid production. The 10 and 100 kDa chitosan treatments at 20 mg L-1 suggested higher protein contents than the other treatments. Chitosan's molecular weight and concentration influenced the relative ratios of functional groups in cell wall lignin. Ten kDa chitosan treatments triggered lignin production better than the other chitosan variants. The results showed that its molecular weight plays a role in the differentiation of chitosan's effects on the biomolecule pattern of E. vesicaria ssp. sativa leaves. However, none of the treatments induced significant changes in the peak positions, indicating that ex vitro chitosan treatment did not induce structural changes in the monitored biomolecules. The results also suggested that 10 kDa chitosan at 5 mg L-1 could be a better option than the other treatments tested, considering reducing the chemical use and cost in the cultivation process of the plant.
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Affiliation(s)
- Arda Acemi
- Department of Biology, Faculty of Arts and Sciences, Kocaeli University, 41001, İzmit, Kocaeli, Turkey.
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Ma X, Wang K, Chou KC, Li Q, Lu X. Conditional Generative Adversarial Network for Spectral Recovery to Accelerate Single-Cell Raman Spectroscopic Analysis. Anal Chem 2022; 94:577-582. [DOI: 10.1021/acs.analchem.1c04263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Xiangyun Ma
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kaidi Wang
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
| | - Keng C. Chou
- Department of Chemistry, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Qifeng Li
- School of Precision Instrument and Optoelectronics Engineering, Tianjin University, Tianjin 300072, China
| | - Xiaonan Lu
- Department of Food Science and Agricultural Chemistry, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec H9X 3V9, Canada
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Machine learning analysis of SERS fingerprinting for the rapid determination of Mycobacterium tuberculosis infection and drug resistance. Comput Struct Biotechnol J 2022; 20:5364-5377. [PMID: 36212533 PMCID: PMC9526180 DOI: 10.1016/j.csbj.2022.09.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/21/2022] [Accepted: 09/21/2022] [Indexed: 11/21/2022] Open
Abstract
Handheld Raman spectrometer is able to generate SERS spectra with sufficient quality for Mycobacterium tuberculosis detection. It is feasible to accurately discriminate Mtb-positive sputum from Mtb-negative sputum through SERS spectrometry. Pulmonary and extra-pulmonary Mtb strains were able to be accurately distinguished via SERS spectral analysis. Profiling of antibiotic resistance of Mtb strains was successfully achieved through machine learning analysis of SERS spectra.
Over the past decades, conventional methods and molecular assays have been developed for the detection of tuberculosis (TB). However, these techniques suffer limitations in the identification of Mycobacterium tuberculosis (Mtb), such as long turnaround time and low detection sensitivity, etc., not even mentioning the difficulty in discriminating antibiotics-resistant Mtb strains that cause great challenges in TB treatment and prevention. Thus, techniques with easy implementation for rapid diagnosis of Mtb infection are in high demand for routine TB diagnosis. Due to the label-free, low-cost and non-invasive features, surface enhanced Raman spectroscopy (SERS) has been extensively investigated for its potential in bacterial pathogen identification. However, at current stage, few studies have recruited handheld Raman spectrometer to discriminate sputum samples with or without Mtb, separate pulmonary Mtb strains from extra-pulmonary Mtb strains, or profile Mtb strains with different antibiotic resistance characteristics. In this study, we recruited a set of supervised machine learning algorithms to dissect different SERS spectra generated via a handheld Raman spectrometer with a focus on deep learning algorithms, through which sputum samples with or without Mtb strains were successfully differentiated (5-fold cross-validation accuracy = 94.32%). Meanwhile, Mtb strains isolated from pulmonary and extra-pulmonary samples were effectively separated (5-fold cross-validation accuracy = 99.86%). Moreover, Mtb strains with different drug-resistant profiles were also competently distinguished (5-fold cross-validation accuracy = 99.59%). Taken together, we concluded that, with the assistance of deep learning algorithms, handheld Raman spectrometer has a high application potential for rapid point-of-care diagnosis of Mtb infections in future.
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Pielesz A, Ślusarczyk C, Sieradzka M, Kukulski T, Biniaś D, Fryczkowski R, Bobiński R, Waksmańska W. Graphene Oxide as a Collagen Modifier of Amniotic Membrane and Burnt Skin. Nanotechnol Sci Appl 2021; 14:221-235. [PMID: 34908830 PMCID: PMC8665888 DOI: 10.2147/nsa.s343540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/17/2021] [Indexed: 12/11/2022] Open
Abstract
Introduction The aim of this interdisciplinary study was to answer the question of whether active antioxidants as graphene oxide (GO), sodium ascorbate, and L-ascorbic acid modify at a molecular and supramolecular level the tissue of pathological amnion and the necrotic eschar degraded in thermal burn. We propose new solutions of modifiers based on GO that will become innovative ingredients to be used in transplants (amnion) and enhance regeneration of epidermis degraded in thermal burn. Methods A Nicolet 6700 spectrophotometer with Omnic software and the EasiDiff diffusion accessory were used in FTIR spectroscopic analysis. A Nicolet Magna-IR 860 spectrometer with an FT Raman accessory was used to record the Raman spectra of the samples. The surface of the samples was examined using a Phenom ProX scanning electron microscope with an energy-dispersive X-ray spectroscopy detector to diagnose and illustrate morphological effects on skin and amnion samples. SAXS measurements were carried out with a compact Kratky camera equipped with the SWAXS optical system. Results Characterisation of amide I-III regions, important for molecular structure, on both FTIR and FTR spectra revealed distinct shifts, testifying to organization of protein structure after GO modification. A wide lipid band associated with ester-group vibrations in phospholipids of cell membranes and vibrations of the carbonyl group of GO in the 1,790-1,720 cm-1 band were observed in the spectra of thermally degraded and GO-modified epidermis and pathological amnion. SAXS studies revealed that GO caused a significant change in the structure of the burnt skin, but its influence on the structure of the amnion was weak. Conclusion Modification of burn-damaged epidermis and pathological amnion by means of GO results in stabilization and regeneration of tissue at the level of molecular (FTIR, FTR) and supramolecular (SAXS) interactions.
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Affiliation(s)
- Anna Pielesz
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Czesław Ślusarczyk
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Marta Sieradzka
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Tomasz Kukulski
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Dorota Biniaś
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Ryszard Fryczkowski
- University of Bielsko-Biała, Faculty of Materials, Civil and Environmental Engineering, Bielsko-Biała, 43-300, Poland
| | - Rafał Bobiński
- University of Bielsko-Biała, Faculty of Health Sciences, Bielsko-Biała, 43-300, Poland
| | - Wioletta Waksmańska
- University of Bielsko-Biała, Faculty of Health Sciences, Bielsko-Biała, 43-300, Poland
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Li B, Wu Y, Wang Z, Xing M, Xu W, Zhu Y, Du P, Wang X, Yang H. Non-invasive diagnosis of Crohn's disease based on SERS combined with PCA-SVM. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:5264-5273. [PMID: 34665186 DOI: 10.1039/d1ay01377g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Crohn's disease (CD) is an idiopathic chronic inflammatory bowel disease without a cure. Most of the CD patients are firstly diagnosed by invasive endoscopy, and clinical and pathological examinations are further required to confirm the diagnosis. Hence, the development of a non-invasive, rapid and accurate diagnosis method for CD patients is essential. In this study, urine samples from 95 CD patients (including 58 active CD (aCD) patients and 37 inactive CD (iCD) patients) and 48 healthy controls (HC) were investigated by surface-enhanced Raman spectroscopy (SERS). The statistical analysis of the three groups (i.e., CD/HC, aCD/HC and iCD/HC) was performed on the measured data. Principal component analysis (PCA)-support vector machine (SVM) and PCA-linear discriminant analysis (LDA) were then employed to establish classification models to distinguish between patients and HC. For the average SERS spectra of patients and HC, the Raman peaks belonging to lipids, proteins and nucleic acids were stronger in patients than those in HC. It showed that the classification accuracy of CD/HC based on PCA-SVM was higher than that of PCA-LDA (82.5% vs. 69.9%). And the classification accuracy of aCD/HC based on PCA-SVM was higher than that of iCD/HC (86.8% vs. 76.5%). The classification model we established distinguished between aCD and HC with 86.2% sensitivity and 87.5% specificity. It indicates that the metabolic change of patients could be identified by measuring urine with SERS, and aCD and HC could be distinguished more effectively. Our findings are helpful for clinicians to diagnose CD patients and monitor the progress and recurrence of the disease.
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Affiliation(s)
- Bingyan Li
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Yaling Wu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China.
| | - Zijie Wang
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Mengmeng Xing
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Weimin Xu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Yilian Zhu
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Peng Du
- Department of Colorectal Surgery, Xinhua Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200092, China
| | - Xiaolei Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China.
| | - Huinan Yang
- School of Energy and Power Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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Solevåg AL, Zykova SN, Thorsby PM, Schmölzer GM. Metabolomics to Diagnose Oxidative Stress in Perinatal Asphyxia: Towards a Non-Invasive Approach. Antioxidants (Basel) 2021; 10:antiox10111753. [PMID: 34829624 PMCID: PMC8615205 DOI: 10.3390/antiox10111753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 11/16/2022] Open
Abstract
There is a need for feasible and non-invasive diagnostics in perinatal asphyxia. Metabolomics is the study of small molecular weight products of cellular metabolism that may, directly and indirectly, reflect the level of oxidative stress. Saliva analysis is a novel approach that has a yet unexplored potential in metabolomics in perinatal asphyxia. The aim of this review was to give an overview of metabolomics studies of oxidative stress in perinatal asphyxia, particularly searching for studies analyzing non-invasively collected biofluids including saliva. We searched the databases PubMed/Medline and included 11 original human and 4 animal studies. In perinatal asphyxia, whole blood, plasma, and urine are the most frequently used biofluids used for metabolomics analyses. Although changes in oxidative stress-related salivary metabolites have been reported in adults, the utility of this approach in perinatal asphyxia has not yet been explored. Human and animal studies indicate that, in addition to antioxidant enzymes, succinate and hypoxanthine, as well acylcarnitines may have discriminatory diagnostic and prognostic properties in perinatal asphyxia. Researchers may utilize the accumulating evidence of discriminatory metabolic patterns in perinatal asphyxia to develop bedside methods to measure oxidative stress metabolites in perinatal asphyxia. Although only supported by indirect evidence, saliva might be a candidate biofluid for such point-of-care diagnostics.
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Affiliation(s)
- Anne Lee Solevåg
- The Department of Paediatric and Adolescent Medicine, Oslo University Hospital, 0424 Nydalen, Norway
- Correspondence: ; Tel.: +47-4146-9314
| | - Svetlana N. Zykova
- Biochemical Endocrinology and Metabolism Research Group, The Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, 0424 Nydalen, Norway; (S.N.Z.); (P.M.T.)
| | - Per Medbøe Thorsby
- Biochemical Endocrinology and Metabolism Research Group, The Hormone Laboratory, Department of Medical Biochemistry, Oslo University Hospital, 0424 Nydalen, Norway; (S.N.Z.); (P.M.T.)
| | - Georg M. Schmölzer
- Centre for the Studies of Asphyxia and Resuscitation, Neonatal Research Unit, Royal Alexandra Hospital, Edmonton, AB 23821, Canada;
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB 23821, Canada
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Osiecka-Drewniak N, Czarnecki MA, Galewski Z. Investigation of phase transitions in liquid crystal 12BBAA using window clustering of infrared spectra. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Collagen orientation probed by polarized Raman spectra can serve as differential diagnosis indicator between different grades of meniscus degeneration. Sci Rep 2021; 11:20299. [PMID: 34645874 PMCID: PMC8514572 DOI: 10.1038/s41598-021-99569-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/19/2021] [Indexed: 11/08/2022] Open
Abstract
The purpose of the present study was to analyze normal and degenerated menisci with Raman methodology on thin sections of formalin fixed paraffin embedding tissues and to correlate the Raman findings with the grade of meniscus degeneration. Menisci (n = 27) were removed from human knee joints after total knee replacement or meniscectomy. Following routine histopathological analysis to determine the grade of meniscal lesions obtained from healthy and degenerated formaline fixed paraffin embedded (FFPE) meniscal sections, Raman polarization approach was applied to evaluate the orientation of collagen fibrils in different levels of the same 5 μm thick FFPE meniscal tissue sections, used for histopathological assessment. We collected Raman spectra in two different polarization geometries, v-HH and v-VV, and calculated the mean value of the v-HH/v-VV intensity ratio of two Raman bands, sensitive and non-sensitive to the molecular orientation. The collagen specific amide I band at 1665 cm-1, has the higher sensitivity dependence on the Raman polarization. The mean values of ratio v-HH/v-VV of the 1665 cm-1 peak intensity was significantly higher in healthy, mean ± SD: 2.56 ± 0.46, compared to degenerated menisci, mean ± SD: 1.85 ± 0.42 (p = 0.0014). The mean values of v-HH/v-VV intensity ratio were 2.18 and 1.50 for low and high degenerated menisci, respectively (p < 0.0001). The difference of peak intensities in the two laser polarizations is decreased in the degenerated meniscus; this difference is diminishing as the degeneration increases. The v-HH/v-VV ratio was also of significant difference in low as compared to control and high grade meniscus lesions (p = 0.036 and p < 0.0001, respectively) offering valuable information for the approach of its biology and function. In the present study we showed that the 5 μm thick sections can be used for Raman analysis of meniscal tissue with great reliability, in terms of sensitivity, specificity, false-negative and false-positive results. Our data introduce the interesting hypothesis that compact portable Raman microscopy on tissue sections can be used intra-operatively for fast diagnosis and hence, accurate procedure design in the operating room.
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Finding reduced Raman spectroscopy fingerprint of skin samples for melanoma diagnosis through machine learning. Artif Intell Med 2021; 120:102161. [PMID: 34629149 DOI: 10.1016/j.artmed.2021.102161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/23/2022]
Abstract
Early-stage detection of cutaneous melanoma can vastly increase the chances of cure. Excision biopsy followed by histological examination is considered the gold standard for diagnosing the disease, but requires long high-cost processing time, and may be biased, as it involves qualitative assessment by a professional. In this paper, we present a new machine learning approach using raw data for skin Raman spectra as input. The approach is highly efficient for classifying benign versus malignant skin lesions (AUC 0.98, 95% CI 0.97-0.99). Furthermore, we present a high-performance model (AUC 0.97, 95% CI 0.95-0.98) using a miniaturized spectral range (896-1039 cm-1), thus demonstrating that only a single fragment of the biological fingerprint Raman region is needed for producing an accurate diagnosis. These findings could favor the future development of a cheaper and dedicated Raman spectrometer for fast and accurate cancer diagnosis.
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Cao T, Weaver AA, Baek S, Jia J, Shrout JD, Bohn PW. Depth distributions of signaling molecules in Pseudomonas aeruginosa biofilms mapped by confocal Raman microscopy. J Chem Phys 2021; 154:204201. [PMID: 34241187 DOI: 10.1063/5.0052785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen implicated in both acute and chronic diseases, which resists antibiotic treatment, in part by forming physical and chemical barriers such as biofilms. Here, we explore the use of confocal Raman imaging to characterize the three-dimensional (3D) spatial distribution of alkyl quinolones (AQs) in P. aeruginosa biofilms by reconstructing depth profiles from hyperspectral Raman data. AQs are important to quorum sensing (QS), virulence, and other actions of P. aeruginosa. Three-dimensional distributions of three different AQs (PQS, HQNO, and HHQ) were observed to have a significant depth, suggesting 3D anisotropic shapes-sheet-like rectangular solids for HQNO and extended cylinders for PQS. Similar to observations from 2D imaging studies, spectral features characteristic of AQs (HQNO or PQS) and the amide I vibration from peptide-containing species were found to correlate with the PQS cylinders typically located at the tips of the HQNO rectangular solids. In the QS-deficient mutant lasIrhlI, a small globular component was observed, whose highly localized nature and similarity in size to a P. aeruginosa cell suggest that the feature arises from HHQ localized in the vicinity of the cell from which it was secreted. The difference in the shapes and sizes of the aggregates of the three AQs in wild-type and mutant P. aeruginosa is likely related to the difference in the cellular response to growth conditions, environmental stress, metabolic levels, or other structural and biochemical variations inside biofilms. This study provides a new route to characterizing the 3D structure of biofilms and shows the potential of confocal Raman imaging to elucidate the nature of heterogeneous biofilms in all three spatial dimensions. These capabilities should be applicable as a tool in studies of infectious diseases.
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Affiliation(s)
- Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Abigail A Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Seol Baek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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Theakstone AG, Brennan PM, Jenkinson MD, Mills SJ, Syed K, Rinaldi C, Xu Y, Goodacre R, Butler HJ, Palmer DS, Smith BR, Baker MJ. Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours. Cancers (Basel) 2021; 13:cancers13153851. [PMID: 34359751 PMCID: PMC8345395 DOI: 10.3390/cancers13153851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.
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Affiliation(s)
- Ashton G. Theakstone
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK;
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
- Department of Pharmacology & Therapeutics, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha J. Mills
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Holly J. Butler
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - David S. Palmer
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK
| | - Benjamin R. Smith
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - Matthew J. Baker
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
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Lima C, Muhamadali H, Goodacre R. The Role of Raman Spectroscopy Within Quantitative Metabolomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:323-345. [PMID: 33826853 DOI: 10.1146/annurev-anchem-091420-092323] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ninety-four years have passed since the discovery of the Raman effect, and there are currently more than 25 different types of Raman-based techniques. The past two decades have witnessed the blossoming of Raman spectroscopy as a powerful physicochemical technique with broad applications within the life sciences. In this review, we critique the use of Raman spectroscopy as a tool for quantitative metabolomics. We overview recent developments of Raman spectroscopy for identification and quantification of disease biomarkers in liquid biopsies, with a focus on the recent advances within surface-enhanced Raman scattering-based methods. Ultimately, we discuss the applications of imaging modalities based on Raman scattering as label-free methods to study the abundance and distribution of biomolecules in cells and tissues, including mammalian, algal, and bacterial cells.
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Affiliation(s)
- Cassio Lima
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular, and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
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Chen S, Wang C, Zhu R, Zhu S, Zhang G. Predicting prognosis in acute myeloid leukemia patients by surface-enhanced Raman spectroscopy. Nanomedicine (Lond) 2021; 16:1873-1885. [PMID: 34269596 DOI: 10.2217/nnm-2021-0199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: To develop a timely and accurate method for predicting acute myeloid leukemia (AML) prognosis after chemotherapy treatment by surface-enhanced Raman spectroscopy (SERS). Methods: Biomolecular differences between AML patients with good and poor prognosis and individuals without AML were investigated based on SERS measurements of bone marrow supernatant fluid samples. Multivariate analysis was implemented on the SERS measurements to establish an AML prognostic model. Results: Significant differences in amino acid, saccharide and lipid levels were observed between AML patients with good and poor prognoses. The AML prognostic model achieved a prediction accuracy of 84.78%. Conclusion: The proposed method could be a potential diagnostic tool for timely and precise prediction of AML prognosis.
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Affiliation(s)
- Shuo Chen
- College of Medicine & Biological Information Engineering, Northeastern University, No. 500 Wisdom Street, Shenyang, 110169, China.,Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, No. 500 Wisdom Street, Shenyang, 110169, China
| | - Chunmeng Wang
- College of Medicine & Biological Information Engineering, Northeastern University, No. 500 Wisdom Street, Shenyang, 110169, China
| | - Ruochen Zhu
- College of Medicine & Biological Information Engineering, Northeastern University, No. 500 Wisdom Street, Shenyang, 110169, China
| | - Shanshan Zhu
- Research Institute for Medical & Biological Engineering, Ningbo University, No. 818 Fenghua Road, Ningbo, 315211, China
| | - Guojun Zhang
- Department of Hematology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Shenyang, 110022, China
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Kochan K, Bedolla DE, Perez-Guaita D, Adegoke JA, Chakkumpulakkal Puthan Veettil T, Martin M, Roy S, Pebotuwa S, Heraud P, Wood BR. Infrared Spectroscopy of Blood. APPLIED SPECTROSCOPY 2021; 75:611-646. [PMID: 33331179 DOI: 10.1177/0003702820985856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.
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Affiliation(s)
- Kamila Kochan
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Diana E Bedolla
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - David Perez-Guaita
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - John A Adegoke
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | | | - Miguela Martin
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Supti Roy
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Savithri Pebotuwa
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Philip Heraud
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Bayden R Wood
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
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Chen Y, Xie T, Ye M, Lai Q, Wang Y, Xu Y, Chen W, Zheng W, Feng S, Huang Y. Combination of pathological and spectroscopic characterization to promote diagnosis of retinal pigment epithelium-Bruch's membrane complex in a diabetic rat model. BIOMEDICAL OPTICS EXPRESS 2021; 12:2221-2235. [PMID: 33996225 PMCID: PMC8086466 DOI: 10.1364/boe.419716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 05/04/2023]
Abstract
Diabetic retinopathy (DR) is a common condition of diabetes, and approaches to detecting early DR using the unique characteristics of the retinal pigment epithelium-Bruch's membrane complex (RBC) have increasingly attracted attention. A diabetic model was established in Sprague-Dawley rats via streptozocin (STZ) injection for 1 (DM1) and 6 months (DM6), confirmed by weekly blood glucose measurement. Serum and retinal tissue-based advanced glycation endproducts (AGE) levels significantly elevated in diabetic rats, and RBC was evaluated by transmission electron microscopy and Raman spectroscopy. The results showed that whole Raman spectra and all marked band intensities could respectively achieve almost equal and accurate discrimination of all animal groups, along with the determination of important molecules from the band data. Further quantitative analyses indicated series of metabolic disturbance due to hyperglycemia were involved while the body self-regulation mechanism still played a role with different effects during the disease progression. Given this, Raman spectroscopy can reliably distinguish the early characterization of DR in addition to providing intrinsic key molecules that is sensitive to identify the early disease progression.
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Affiliation(s)
- Yang Chen
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou 350004, China
| | - Ting Xie
- Department of Ophthalmology & Optometry, Fujian Medical University, Fuzhou 350004, China
| | - Minlu Ye
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou 350004, China
| | - Qiaoling Lai
- Department of Ophthalmology & Optometry, Fujian Medical University, Fuzhou 350004, China
| | - Yuting Wang
- Department of Laboratory Medicine, Fujian Medical University, Fuzhou 350004, China
| | - Yunchao Xu
- Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350007, China
| | - Wenyi Chen
- Department of Ophthalmology & Optometry, Fujian Medical University, Fuzhou 350004, China
| | - Weidong Zheng
- Department of Ophthalmology, The First Affiliated Hospital of Fujian Medical University, Fuzhou 350004, China
| | - Shangyuan Feng
- Key Laboratory of Optoelectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350007, China
| | - Yan Huang
- Department of Ophthalmology & Optometry, Fujian Medical University, Fuzhou 350004, China
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48
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Differential responses of sorghum genotypes to drought stress revealed by physio-chemical and transcriptional analysis. Mol Biol Rep 2021; 48:2453-2462. [PMID: 33755850 DOI: 10.1007/s11033-021-06279-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Sorghum is an essential food crop for millions of people in the semi-arid regions of the world, where its production is severely limited by drought stress. Drought in the early stages of crop growth and development irreversibly interferes, which leads to poor yield. The effect of drought stress in sorghum was studied at physiological, biochemical, and molecular levels in a set of two genotypes differing in their tolerance to drought. Drought stress was imposed by restraining water for 10 days on 25 days old seedlings. A significant influence of water stress was observed on the considered morpho-physiological and biochemical traits. The genotype DRT1019 exhibited physiological and biochemical indicators of drought avoidance through delayed leaf rolling, osmotic adjustment, ideal gas-exchange system, solute accumulation, an increased level of enzyme synthesis and root trait expression as compared to the ICSV95022 genotype. Furthermore, differences in the metabolite changes viz. total carbohydrate, total amides, and lipids were found between the two genotypes under drought stress. In addition, transcript profiling of potential candidate drought genes such as SbTIP3-1, SbDHN1, SbTPS, and SbDREB1A revealed up-regulation in DRT1019, which corresponded with other important physiological and biochemical parameters exhibited in the genotype. In conclusion, this study provides an improved understanding of whole plant response to drought stress in sorghum. Additionally, our results provide promising candidate genes for drought tolerance in sorghum that can be used as potential markers for drought tolerance breeding programs.
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Weng S, Hu X, Wang J, Tang L, Li P, Zheng S, Zheng L, Huang L, Xin Z. Advanced Application of Raman Spectroscopy and Surface-Enhanced Raman Spectroscopy in Plant Disease Diagnostics: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2950-2964. [PMID: 33677962 DOI: 10.1021/acs.jafc.0c07205] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plant diseases result in 20-40% of agricultural loss every year worldwide. Timely detection of plant diseases can effectively prevent the development and spread of diseases and ensure the agricultural yield. High-throughput and rapid methods are in great demand. This review investigates the advanced application of Raman spectroscopy (RS) and surface-enhanced Raman spectroscopy (SERS) in the detection of plant diseases. The determination of bacterial diseases and stress-induced diseases, fungal diseases, viral diseases, pests in beans, and mycotoxins related to plant diseases using RS and SERS are discussed in detail. Then, biomarkers for RS and SERS detection are analyzed with regard to plant disease diagnosis. Finally, the advantages and challenges are further illustrated. Additionally, potential alternatives are proposed for the challenges. The review is expected to provide a reference and guidance for the use of RS and SERS in plant disease diagnostics.
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Affiliation(s)
- Shizhuang Weng
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Xujin Hu
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Jinghong Wang
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Le Tang
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Pan Li
- Hefei Institute of Physical Science, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031, People's Republic of China
| | - Shouguo Zheng
- Hefei Institute of Physical Science, Chinese Academy of Sciences, 350 Shushanhu Road, Hefei 230031, People's Republic of China
| | - Ling Zheng
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Linsheng Huang
- National Engineering Research Center for Agro-Ecological Big Data Analysis & Application, Anhui University, 111 Jiulong Road, Hefei 230601, People's Republic of China
| | - Zhenghua Xin
- College of Information Engineering, Suzhou University, 1769 Xuefu Avenue, Suzhou, People's Republic of China
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50
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Rivera-Velez SM, Navas J, Villarino NF. Applying metabolomics to veterinary pharmacology and therapeutics. J Vet Pharmacol Ther 2021; 44:855-869. [PMID: 33719079 DOI: 10.1111/jvp.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Metabolomics is the large-scale study of low-molecular-weight substances in a biological system in a given physiological state at a given time point. Metabolomics can be applied to identify predictors of inter-individual variability in drug response, provide clinicians with data useful for decision-making processes in drug selection, and inform about the pharmacokinetics and pharmacodynamics of a drug. It is, therefore, an exceptional approach for gaining new understanding effects in the field of comparative veterinary pharmacology. However, the incorporation of metabolomics into veterinary pharmacology and toxicology is not yet widespread, and this is probably, at least in part, a result of its highly multidisciplinary nature. This article reviews the potential applications of metabolomics in veterinary pharmacology and therapeutics. It integrates key concepts for designing metabolomics studies and analyzing and interpreting metabolomics data, providing solid foundations for applying metabolomics to the study of drugs in all veterinary species.
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Affiliation(s)
- Sol M Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, Saint Petersburg, Florida, USA
| | - Jinna Navas
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
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