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Cui Z, Li Y, Jing X, Luan X, Liu N, Liu J, Meng Y, Xu J, Valentine DL. Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas. J Hazard Mater 2024; 469:133904. [PMID: 38422739 DOI: 10.1016/j.jhazmat.2024.133904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/30/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.
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Affiliation(s)
- Zhisong Cui
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China.
| | - Yingchao Li
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Xiaoyan Jing
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Xiao Luan
- State Key Laboratory of Simulation and Regulation of Water Cycle in River Basin, China Institute of Water Resources and Hydropower Research, Beijing 100048, People's Republic of China
| | - Na Liu
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Jinyan Liu
- Marine Bioresource and Environment Research Center, Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources of China, Qingdao 266061, People's Republic of China
| | - Yu Meng
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, People's Republic of China
| | - David L Valentine
- Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, CA 93106, USA.
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Hajab H, Anwar A, Nawaz H, Majeed MI, Alwadie N, Shabbir S, Amber A, Jilani MI, Nargis HF, Zohaib M, Ismail S, Kamal A, Imran M. Surface-enhanced Raman spectroscopy of the filtrate portions of the blood serum samples of breast cancer patients obtained by using 30 kDa filtration device. Spectrochim Acta A Mol Biomol Spectrosc 2024; 311:124046. [PMID: 38364514 DOI: 10.1016/j.saa.2024.124046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/04/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Raman spectroscopy is reliable tool for analyzing and exploring early disease diagnosis related to body fluids, such as blood serum, which contain low molecular weight fraction (LMWF) and high molecular weight fraction (HMWF) proteins. The disease biomarkers consist of LMWF which are dominated by HMWF hence their analysis is difficult. In this study, in order to overcome this issue, centrifugal filter devices of 30 kDa were used to obtain filtrate and residue portions obtained from whole blood serum samples of control and breast cancer diagnosed patients. The filtrate portions obtained in this way are expected to contain the marker proteins of breast cancer of the size below this filter size. These may include prolactin, Microphage migration inhabitation factor (MIF), γ-Synuclein, BCSG1, Leptin, MUC1, RS/DJ-1 present in the centrifuged blood serum (filtrate portions) which are then analyzed by the SERS technique to recognize the SERS spectral characteristics associated with the progression of breast cancer in the samples of different stages as compared to the healthy ones. The key intention of this study is to achieve early-stage breast cancer diagnosis through the utilization of Surface Enhanced Raman Spectroscopy (SERS) after the centrifugation of healthy and breast cancer serum samples with Amicon ultra-filter devices of 30 kDa. The silver nanoparticles with high plasmon resonance are used as a substrate for SERS analysis. Principal Component Analysis (PCA) and Partial Least Discriminant Analysis (PLS-DA) models are utilized as spectral classification tools to assess and predict rapid, reliable, and non-destructive SERS-based analysis. Notably, they were particularly effective in distinguishing between different SERS spectral groups of the cancerous and non-cancerous samples. By comparing all these spectral data sets to each other PLSDA shows the 79 % accuracy, 76 % specificity, and 81 % sensitivity in samples with AUC value of AUC = 0.774 SERS has proven to be a valuable technique for the rapid identification of the SERS spectral features of blood serum and its filtrate fractions from both healthy individuals and those with breast cancer, aiding in disease diagnosis.
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Affiliation(s)
- Hawa Hajab
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ayesha Anwar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan.
| | - Najah Alwadie
- Department of Physics, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia.
| | - Sana Shabbir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Arooj Amber
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Hafiza Faiza Nargis
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Zohaib
- Department of Zoology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Sidra Ismail
- Medical College, Foundation University Islamabad, Pakistan
| | - Abida Kamal
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Imran
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, Saudi Arabia
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Schultze-Rhonhof L, Marzi J, Carvajal Berrio DA, Holl M, Braun T, Schäfer-Ruoff F, Andress J, Bachmann C, Templin M, Brucker SY, Schenke-Layland K, Weiss M. Human tissue-resident peritoneal macrophages reveal resistance towards oxidative cell stress induced by non-invasive physical plasma. Front Immunol 2024; 15:1357340. [PMID: 38504975 PMCID: PMC10949891 DOI: 10.3389/fimmu.2024.1357340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 02/14/2024] [Indexed: 03/21/2024] Open
Abstract
In the context of multimodal treatments for abdominal cancer, including procedures such as cytoreductive surgery and intraperitoneal chemotherapy, recurrence rates remain high, and long-term survival benefits are uncertain due to post-operative complications. Notably, treatment-limiting side effects often arise from an uncontrolled activation of the immune system, particularly peritoneally localized macrophages, leading to massive cytokine secretion and phenotype changes. Exploring alternatives, an increasing number of studies investigated the potential of plasma-activated liquids (PAL) for adjuvant peritoneal cancer treatment, aiming to mitigate side effects, preserve healthy tissue, and reduce cytotoxicity towards non-cancer cells. To assess the non-toxicity of PAL, we isolated primary human macrophages from the peritoneum and subjected them to PAL exposure. Employing an extensive methodological spectrum, including flow cytometry, Raman microspectroscopy, and DigiWest protein analysis, we observed a pronounced resistance of macrophages towards PAL. This resistance was characterized by an upregulation of proliferation and anti-oxidative pathways, countering PAL-derived oxidative stress-induced cell death. The observed cellular effects of PAL treatment on human tissue-resident peritoneal macrophages unveil a potential avenue for PAL-derived immunomodulatory effects within the human peritoneal cavity. Our findings contribute to understanding the intricate interplay between PAL and macrophages, shedding light on the promising prospects for PAL in the adjuvant treatment of peritoneal cancer.
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Affiliation(s)
| | - Julia Marzi
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, University of Tübingen, Tübingen, Germany
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Daniel Alejandro Carvajal Berrio
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, University of Tübingen, Tübingen, Germany
| | - Myriam Holl
- Department of Women’s Health Tübingen, University of Tübingen, Tübingen, Germany
| | - Theresa Braun
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
- University Development, Research and Transfer, University of Konstanz, Konstanz, Germany
| | - Felix Schäfer-Ruoff
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Jürgen Andress
- Department of Women’s Health Tübingen, University of Tübingen, Tübingen, Germany
| | - Cornelia Bachmann
- Department of Women’s Health Tübingen, University of Tübingen, Tübingen, Germany
| | - Markus Templin
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Sara Y. Brucker
- Department of Women’s Health Tübingen, University of Tübingen, Tübingen, Germany
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, University of Tübingen, Tübingen, Germany
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Martin Weiss
- Department of Women’s Health Tübingen, University of Tübingen, Tübingen, Germany
- Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
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Guo G, Guo C, Qie X, He D, Meng S, Su L, Liang S, Yin S, Yu G, Zhang Z, Hua X, Song Y. Correlation analysis between Raman spectral signature and transcriptomic features of carbapenem-resistant Klebsiella pneumoniae. Spectrochim Acta A Mol Biomol Spectrosc 2024; 308:123699. [PMID: 38043297 DOI: 10.1016/j.saa.2023.123699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/09/2023] [Accepted: 11/26/2023] [Indexed: 12/05/2023]
Abstract
The Raman microspectroscopy technology has been successfully applied to evaluate the molecular composition of living cells for identifying cell types and states, but the rationale behind it was not well investigated. In this study, we acquired single-cell Raman spectra (SCRS) of three Klebsiella pneumoniae (K. pneumoniae) strains with different Carbapenem resistant mechanisms and analyzed them with machine learning algorithm. Two carbapenem resistant Klebsiella pneumoniae (CRKP) strains can be successfully distinguished from susceptible strain and CRKP with KPC or IMP carbapenemases can be classified with an overall accuracy achieving 100 %. Furthermore, we performed a correlation analysis between transcriptome and Raman spectra, and found that Raman shifts such as 752 and 1039 cm-1 highly correlated with drug resistance genes expression and could be regarded as Raman biomarkers for CRKP with different mechanisms. The findings of the study provide a theoretical basis for identifying the relationship between Raman spectra and transcriptome of bacteria, as well as a novel method for rapid identification of CRKP and their carbapenemases types.
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Affiliation(s)
- Guanghui Guo
- The Third People's Hospital of Longgang District, Shenzhen 518112, China
| | - Chen Guo
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China; Nanjing Police University, Nanjing 210023, China
| | - Dahui He
- The Third People's Hospital of Longgang District, Shenzhen 518112, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China
| | - Liqing Su
- The Third People's Hospital of Longgang District, Shenzhen 518112, China
| | | | - Sanjun Yin
- Health Time Gene Institute, Shenzhen 518000, China
| | - Guangchao Yu
- The first affiliated hospital of Jinan university, Guangzhou 510630, China
| | - Zhiqiang Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310016, China; Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Yizhi Song
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou 215163, China; Chongqing Guoke Medical Technology Development Co., Ltd, Chongqing 400799, China.
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5
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Hu J, Chen GJ, Xue C, Liang P, Xiang Y, Zhang C, Chi X, Liu G, Ye Y, Cui D, Zhang D, Yu X, Dang H, Zhang W, Chen J, Tang Q, Guo P, Ho HP, Li Y, Cong L, Shum PP. RSPSSL: A novel high-fidelity Raman spectral preprocessing scheme to enhance biomedical applications and chemical resolution visualization. Light Sci Appl 2024; 13:52. [PMID: 38374161 PMCID: PMC10876988 DOI: 10.1038/s41377-024-01394-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 01/02/2024] [Accepted: 01/23/2024] [Indexed: 02/21/2024]
Abstract
Raman spectroscopy has tremendous potential for material analysis with its molecular fingerprinting capability in many branches of science and technology. It is also an emerging omics technique for metabolic profiling to shape precision medicine. However, precisely attributing vibration peaks coupled with specific environmental, instrumental, and specimen noise is problematic. Intelligent Raman spectral preprocessing to remove statistical bias noise and sample-related errors should provide a powerful tool for valuable information extraction. Here, we propose a novel Raman spectral preprocessing scheme based on self-supervised learning (RSPSSL) with high capacity and spectral fidelity. It can preprocess arbitrary Raman spectra without further training at a speed of ~1 900 spectra per second without human interference. The experimental data preprocessing trial demonstrated its excellent capacity and signal fidelity with an 88% reduction in root mean square error and a 60% reduction in infinite norm ([Formula: see text]) compared to established techniques. With this advantage, it remarkably enhanced various biomedical applications with a 400% accuracy elevation (ΔAUC) in cancer diagnosis, an average 38% (few-shot) and 242% accuracy improvement in paraquat concentration prediction, and unsealed the chemical resolution of biomedical hyperspectral images, especially in the spectral fingerprint region. It precisely preprocessed various Raman spectra from different spectroscopy devices, laboratories, and diverse applications. This scheme will enable biomedical mechanism screening with the label-free volumetric molecular imaging tool on organism and disease metabolomics profiling with a scenario of high throughput, cross-device, various analyte complexity, and diverse applications.
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Affiliation(s)
- Jiaqi Hu
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Gina Jinna Chen
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Chenlong Xue
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Pei Liang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Yanqun Xiang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaokeng Chi
- Department of Nephrology, Chaozhou People's Hospital, Chaozhou, 521011, China
| | - Guoying Liu
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, 510060, China
| | - Yanfang Ye
- Clinical Research Design Division, Sun Yat-sen Memorial Hospital, Guangzhou, Guangdong, 510120, China
| | - Dongyu Cui
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - De Zhang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China
| | - Xiaojun Yu
- School of Automation, Northwestern Polytechnical University, Xi'an, Shaanxi, 710072, China
| | - Hong Dang
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wen Zhang
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Junfan Chen
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Quan Tang
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Penglai Guo
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ho-Pui Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Yuchao Li
- Guangdong Provincial Key Laboratory of Nanophotonic Manipulation, Institute of Nanophotonics, Jinan University, Guangzhou, 511443, China
| | - Longqing Cong
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Perry Ping Shum
- State Key Laboratory of Optical Fiber and Cable Manufacture Technology, Guangdong Key Laboratory of Integrated Optoelectronics Intellisense, Department of EEE, Southern University of Science and Technology, Shenzhen, 518055, China.
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Zhang K, Liu R, Wei X, Wang Z, Huang P. Use of Raman spectroscopy to study rat lung tissues for distinguishing asphyxia from sudden cardiac death. RSC Adv 2024; 14:5665-5674. [PMID: 38357034 PMCID: PMC10865087 DOI: 10.1039/d3ra07684a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Determining asphyxia as the cause of death is crucial but is based on an exclusive strategy because it lacks sensitive and specific morphological characteristics in forensic practice. In some cases where the deceased has underlying heart disease, differentiation between asphyxia and sudden cardiac death (SCD) as the primary cause of death can be challenging. Herein, Raman spectroscopy was employed to detect pulmonary biochemical differences to discriminate asphyxia from SCD in rat models. Thirty-two rats were used to build asphyxia and SCD models, with lung samples collected immediately or 24 h after death. Twenty Raman spectra were collected for each lung sample, and 640 spectra were obtained for further data preprocessing and analysis. The results showed that different biochemical alterations existed in the lung tissues of the rats that died from asphyxia and SCD and could be used to distinguish between the two causes of death. Moreover, we screened and used 8 of the 11 main differential spectral features that maintained their significant differences at 24 h after death to successfully determine the cause of death, even with decomposition and autolysis. Eventually, seven prevalent machine learning classification algorithms were employed to establish classification models, among which the support vector machine exhibited the best performance, with an area under the curve value of 0.9851 in external validation. This study shows the promise of Raman spectroscopy combined with machine learning algorithms to investigate differential biochemical alterations originating from different deaths to aid determining the cause of death in forensic practice.
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Affiliation(s)
- Kai Zhang
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science Shanghai People's Republic of China
- Department of Forensic Pathology, College of Forensic Medicine, NHC Key Laboratory of Forensic Science, Xi'an Jiaotong University Xi'an People's Republic of China
| | - Ruina Liu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University Xi'an People's Republic of China
| | - Xin Wei
- Department of Forensic Pathology, College of Forensic Medicine, NHC Key Laboratory of Forensic Science, Xi'an Jiaotong University Xi'an People's Republic of China
| | - Zhenyuan Wang
- Department of Forensic Pathology, College of Forensic Medicine, NHC Key Laboratory of Forensic Science, Xi'an Jiaotong University Xi'an People's Republic of China
| | - Ping Huang
- Shanghai Key Lab of Forensic Medicine, Key Lab of Forensic Science, Ministry of Justice, China, Academy of Forensic Science Shanghai People's Republic of China
- Institute of Forensic Science, Fudan University Shanghai People's Republic of China
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7
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Rathnayake RAC, Zhao Z, McLaughlin N, Li W, Yan Y, Chen LL, Xie Q, Wu CD, Mathew MT, Wang RR. Machine learning enabled multiplex detection of periodontal pathogens by surface-enhanced Raman spectroscopy. Int J Biol Macromol 2024; 257:128773. [PMID: 38096932 DOI: 10.1016/j.ijbiomac.2023.128773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/02/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
Periodontitis is a chronic inflammation of the periodontium caused by a persistent bacterial infection, resulting in destruction of the supporting structures of teeth. Analysis of microbial composition in saliva can inform periodontal status. Actinobacillus actinomycetemcomitans (Aa), Porphyromonas gingivalis (Pg), and Streptococcus mutans (Sm) are among reported periodontal pathogens, and were used as model systems in this study. Our atomic force microscopic (AFM) study revealed that these pathogens are biological nanorods with dimensions of 0.6-1.1 μm in length and 500-700 nm in width. Current bacterial detection methods often involve complex preparation steps and require labeled reporting motifs. Employing surface-enhanced Raman spectroscopy (SERS), we revealed cell-type specific Raman signatures of these pathogens for label-free detection. It overcame the complexity associated with spectral overlaps among different bacterial species, relying on high signal-to-noise ratio (SNR) spectra carefully collected from pure species samples. To enable simple, rapid, and multiplexed detection, we harnessed advanced machine learning techniques to establish predictive models based on a large set of raw spectra of each bacterial species and their mixtures. Using these models, given a raw spectrum collected from a bacterial suspension, simultaneous identification of all three species in the test sample was achieved at 95.6 % accuracy. This sensing modality can be applied to multiplex detection of a broader range and a larger set of periodontal pathogens, paving the way for hassle-free detection of oral bacteria in saliva with little to no sample preparation.
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Affiliation(s)
- Rathnayake A C Rathnayake
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Zhenghao Zhao
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America
| | - Nathan McLaughlin
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Wei Li
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Yan Yan
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
| | - Liaohai L Chen
- Department of Surgery, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Qian Xie
- Department of Endodontics, University of Illinois Chicago, Chicago, IL, United States of America
| | - Christine D Wu
- Department of Pediatric Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America
| | - Mathew T Mathew
- Department of Restorative Dentistry, University of Illinois Chicago, Chicago, IL 60612, United States of America; Department of Biomedical Sciences, University of Illinois Rockford, Rockford, IL 61107, United States of America
| | - Rong R Wang
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL 60616, United States of America.
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8
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Zhang P, Liu B, Mu X, Xu J, Du B, Wang J, Liu Z, Tong Z. Performance of Classification Models of Toxins Based on Raman Spectroscopy Using Machine Learning Algorithms. Molecules 2023; 29:197. [PMID: 38202780 PMCID: PMC10780255 DOI: 10.3390/molecules29010197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/21/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
Rapid and accurate detection of protein toxins is crucial for public health. The Raman spectra of several protein toxins, such as abrin, ricin, staphylococcal enterotoxin B (SEB), and bungarotoxin (BGT), have been studied. Multivariate scattering correction (MSC), Savitzky-Golay smoothing (SG), and wavelet transform methods (WT) were applied to preprocess Raman spectra. A principal component analysis (PCA) was used to extract spectral features, and the PCA score plots clustered four toxins with two other proteins. The k-means clustering results show that the spectra processed with MSC and MSC-SG methods have the best classification performance. Then, the two data types were classified using partial least squares discriminant analysis (PLS-DA) with an accuracy of 100%. The prediction results of the PCA and PLS-DA and the partial least squares regression model (PLSR) perform well for the fingerprint region spectra. The PLSR model demonstrates excellent classification and regression ability (accuracy = 100%, Rcv = 0.776). Four toxins were correctly classified with interference from two proteins. Classification models based on spectral feature extraction were established. This strategy shows excellent potential in toxin detection and public health protection. These models provide alternative paths for the development of rapid detection devices.
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Affiliation(s)
| | | | | | | | | | | | | | - Zhaoyang Tong
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China; (P.Z.); (B.L.); (X.M.); (J.X.); (B.D.); (J.W.); (Z.L.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Wu Y, Wang Y, He C, Wang Y, Ma J, Lin Y, Zhou L, Xu S, Ye Y, Yin W, Ye J, Lu J. Precise diagnosis of breast phyllodes tumors using Raman spectroscopy: Biochemical fingerprint, tumor metabolism and possible mechanism. Anal Chim Acta 2023; 1283:341897. [PMID: 37977771 DOI: 10.1016/j.aca.2023.341897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/31/2023] [Accepted: 10/09/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Breast fibroadenomas and phyllodes tumors are both fibroepithelial tumors with comparable histological characteristics. However, rapid and precise differential diagnosis is a tough point in clinical pathology. Given the tendency of phyllodes tumors to recur, the difficulty in differential diagnosis with fibroadenomas leads to the difficulty in optimal management for these patients. METHOD In this study, we used Raman spectroscopy to differentiate phyllodes tumors from breast fibroadenomas based on the biochemical and metabolic composition and develop a classification model. The model was validated by 5-fold cross-validation in the training set and tested in an independent test set. The potential metabolic differences between the two types of tumors observed in Raman spectroscopy were confirmed by targeted metabolomic analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS A total of 204 patients with formalin-fixed paraffin-embedded (FFPE) tissue samples, including 100 fibroadenomas and 104 phyllodes tumors were recruited from April 2014 to August 2021. All patients were randomly divided into the training cohort (n = 153) and the test cohort (n = 51). The Raman classification model could differentiate phyllodes tumor versus fibroadenoma with cross-validation accuracy, sensitivity, precision, and area under curve (AUC) of 85.58 % ± 1.77 %, 83.82 % ± 1.01 %, 87.65 % ± 4.22 %, and 93.18 % ± 1.98 %, respectively. When tested in the independent test set, it performed well with the test accuracy, sensitivity, specificity, and AUC of 83.50 %, 86.54 %, 80.39 %, and 90.71 %. Furthermore, the AUC was significantly higher for the Raman model than that for ultrasound (P = 0.0017) and frozen section diagnosis (P < 0.0001). When it came to much more difficult diagnosis between fibroadenoma and benign or small-size phyllodes tumor for pathological examination, the Raman model was capable of differentiating with AUC up to 97.45 % and 95.61 %, respectively. On the other hand, targeted metabolomic analysis, based on fresh-frozen tissue samples, confirmed the differential metabolites (including thymine, dihydrothymine, trans-4-hydroxy-l-proline, etc.) identified from Raman spectra between phyllodes tumor and fibroadenoma. SIGNIFICANCE AND NOVELTY In this study, we obtained the molecular information map of breast phyllodes tumors provided by Raman spectroscopy for the first time. We identified a novel Raman fingerprint signature with the potential to precisely characterize and distinguish phyllodes tumors from fibroadenoma as a quick and accurate diagnostic tool. Raman spectroscopy is expected to further guide the precise diagnosis and optimal treatment of breast fibroepithelial tumors in the future.
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Affiliation(s)
- Yifan Wu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Yaohui Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
| | - Chang He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Yan Wang
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Jiayi Ma
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Yanping Lin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Liheng Zhou
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Shuguang Xu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Yumei Ye
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China
| | - Wenjin Yin
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
| | - Jian Ye
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
| | - Jingsong Lu
- Department of Breast Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
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11
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Amber A, Nawaz H, Bhatti HN, Mushtaq Z. Surface-enhanced Raman spectroscopy for the characterization of different anatomical subtypes of oral cavity cancer. Photodiagnosis Photodyn Ther 2023:103607. [PMID: 37220841 DOI: 10.1016/j.pdpdt.2023.103607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023]
Abstract
BACKGROUND The prognosis for oral cancer patients is still very poor worldwide. Early detection and treatment therapy remain the key issue to be addressed for improved patient survival. The characteristic Raman spectral features associated with the biochemical changes in the blood serum samples can be used for the diagnosis of diseases, particularly for oral cancer. Surface-enhanced Raman spectroscopy (SERS) is a promising technique for non-invasive and early detection of oral cancer by analyzing molecular changes in body fluids. OBJECTIVES To detect oral cavity anatomical subsites (buccal mucosa, cheek, hard palate, lips, mandible, maxilla, tongue and tonsillar region) cancers by using blood serum samples, SERS with principal component analysis is used. MATERIAL AND METHOD SERS is employed with silver nanoparticles for the analysis and detection of oral cancer serum samples by comparing with healthy serum samples. SERS spectra are recorded by Raman instrument and preprocessed using the statistical tool. Principal component analysis (PCA) and Partial least square discriminant analysis (PLS-DA) are used to discriminate between oral cancer serum samples and control serum samples. RESULTS Some major SERS peaks are observed at 1136 cm-1 (Phospholipids) and 1006 cm-1 (Phenylalanine) remain higher in intensities for oral cancer spectra as compared to healthy spectra. The peak at 1241 cm-1 (amide III) is observed only in oral cancer serum samples while absent in healthy serum samples. Higher protein and DNA contents were detected in SERS mean spectra of oral cancer. Moreover, PCA is used to identify the biochemical differences in the form of SERS features which is used to differentiate between oral cancer and healthy blood serum samples, while PLS-DA is used to build differentiation model of oral cancer serum samples and healthy control serum samples. PLS-DA provides successful differentiation with 94% specificity and 95.5% sensitivity. CONCLUSIONS SERS can be used for the diagnosis of oral cancer and to identify metabolic changes that occur during disease development.
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Affiliation(s)
- Arooj Amber
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, (38000), Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, (38000), Pakistan.
| | - Haq Nawaz Bhatti
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, (38000), Pakistan
| | - Zahid Mushtaq
- Department of Biochemistry, University of Agriculture Faisalabad, Faisalabad, (38000), Pakistan
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12
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Nawaz MZ, Nawaz H, Majeed MI, Rashid N, Javed MR, Naz S, Ali MZ, Sabir A, Sadaf N, Rafiq N, Shakeel M, Ali Z, Amin I. Comparison of surface-enhanced Raman spectral data sets of filtrate portions of serum samples of hepatitis B and Hepatitis C infected patients obtained by centrifugal filtration. Photodiagnosis Photodyn Ther 2023; 42:103532. [PMID: 36963645 DOI: 10.1016/j.pdpdt.2023.103532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/13/2023] [Accepted: 03/21/2023] [Indexed: 03/26/2023]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) is an efficient technique which has been used for the analysis of filtrate portions of serum samples of Hepatitis B (HBV) and Hepatitis C (HCV) virus. OBJECTIVES The main reason for this study is to differentiate and compare HBV and HCV serum samples for disease diagnosis through SERS. Hepatitis B and hepatitis C disease biomarkers are more predictable in their centrifuged form as compared in their uncentrifuged form. For differentiation of SERS spectral data sets of hepatitis B, hepatitis C and healthy person principal component analysis (PCA) proved to be a helpful. Centrifugally filtered serum samples of hepatitis B and hepatitis C are clearly differentiated from centrifugally filtered serum samples of healthy individuals by using partial least square discriminant analysis (PLS-DA). METHODOLOGY Serum sample of HBV, HCV and healthy patients were centrifugally filtered to separate filtrate portion for studying biochemical changes in serum sample. The SERS of these samples is performed using silver nanoparticles as substrates to identify specific spectral features of both viral diseases which can be used for the diagnosis and differentiation of these diseases. The purpose of centrifugal filtration of the serum samples of HBV and HCV positive and control samples by using filter membranes of 50 KDa size is to eliminate the proteins bigger than 50 KDa so that their contribution in the SERS spectrum is removed and disease related smaller proteins may be observed. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are statistical tools which were used for the further validation of SERS. RESULTS HBV and HCV centrifugally filtered serum sample were compared and biomarkers including (uracil, phenylalanine, methionine, adenine, phosphodiester, proline, tyrosine, tryptophan, amino acid, thymine, fatty acid, nucleic acid, triglyceride, guanine and hydroxyproline) were identified through PCA and PLS-DA. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) were used as a multivariate data analysis tool for the diagnosis of the characteristic SERS spectral features associated with both types of viral diseases. For the classification and differentiation of centrifugally filtered HBV, HCV, and control serum samples, Principal component analysis is found helpful. Moreover, PLS-DA can classify these two distinct sets of SERS spectral data with 0.90 percent specificity, 0.85 percent precision, and 0.83 percent accuracy. CONCLUSIONS Surface enhanced Raman spectroscopy along with chemometric analysis like PCA and PLS-DA have been successfully differentiated HBV and HCV and healthy individuals' serum samples.
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Affiliation(s)
- Muhammad Zaman Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad (38000), Pakistan.
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad (38000), Pakistan
| | - Saima Naz
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad (38000), Pakistan
| | - Muhammad Zeeshan Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Amina Sabir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Nimra Sadaf
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Nighat Rafiq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Muhammad Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Zain Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad (38000), Pakistan
| | - Imran Amin
- PCR Laboratory, PINUM Hospital, Faisalabad (38000), Pakistan
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13
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Becker L, Lu CE, Montes-Mojarro IA, Layland SL, Khalil S, Nsair A, Duffy GP, Fend F, Marzi J, Schenke-Layland K. Raman microspectroscopy identifies fibrotic tissues in collagen-related disorders via deconvoluted collagen type I spectra. Acta Biomater 2023; 162:278-291. [PMID: 36931422 DOI: 10.1016/j.actbio.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
Fibrosis is a consequence of the pathological remodeling of extracellular matrix (ECM) structures in the connective tissue of an organ. It is often caused by chronic inflammation, which over time, progressively leads to an excess deposition of collagen type I (COL I) that replaces healthy tissue structures, in many cases leaving a stiff scar. Increasing fibrosis can lead to organ failure and death; therefore, developing methods that potentially allow real-time monitoring of early onset or progression of fibrosis are highly valuable. In this study, the ECM structures of diseased and healthy human tissue from multiple organs were investigated for the presence of fibrosis using routine histology and marker-independent Raman microspectroscopy and Raman imaging. Spectral deconvolution of COL I Raman spectra allowed the discrimination of fibrotic and non-fibrotic COL I fibers. Statistically significant differences were identified in the amide I region of the spectral subpeak at 1608 cm-1, which was deemed to be representative for structural changes in COL I fibers in all examined fibrotic tissues. Raman spectroscopy-based methods in combination with this newly discovered spectroscopic biomarker potentially offer a diagnostic approach to non-invasively track and monitor the progression of fibrosis. STATEMENT OF SIGNIFICANCE: Current diagnosis of fibrosis still relies on histopathological examination with invasive biopsy procedures. Although, several non-invasive imaging techniques such as positron emission tomography, single-photon emission computed tomography and second harmonic generation are gradually employed in preclinical or clinical studies, these techniques are limited in spatial resolution and the morphological interpretation highly relies on individual experience and knowledge. In this study, we propose a non-destructive technique, Raman microspectroscopy, to discriminate fibrotic changes of collagen type I based on a molecular biomarker. The changes of the secondary structure of collagen type I can be identified by spectral deconvolution, which potentially can provide an automatic diagnosis for fibrotic tissues in the clinical applicaion.
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Affiliation(s)
- Lucas Becker
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Silcherstr. 7/1, Eberhard Karls University, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany
| | - Chuan-En Lu
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Silcherstr. 7/1, Eberhard Karls University, 72076 Tübingen, Germany
| | | | - Shannon L Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Silcherstr. 7/1, Eberhard Karls University, 72076 Tübingen, Germany
| | - Suzan Khalil
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive South, MRL 3645 Los Angeles, CA, USA
| | - Ali Nsair
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive South, MRL 3645 Los Angeles, CA, USA
| | - Garry P Duffy
- Anatomy & Regenerative Medicine Institute, School of Medicine, College of Medicine, Nursing and Health Sciences, National University of Ireland Galway, H91 TK33, Galway, Ireland
| | - Falko Fend
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Julia Marzi
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Silcherstr. 7/1, Eberhard Karls University, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Silcherstr. 7/1, Eberhard Karls University, 72076 Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany.
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14
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Han S, Chen C, Chen C, Wu L, Wu X, Lu C, Zhang X, Chao P, Lv X, Jia Z, Hou J. Coupling annealed silver nanoparticles with a porous silicon Bragg mirror SERS substrate and machine learning for rapid non-invasive disease diagnosis. Anal Chim Acta 2023; 1254:341116. [PMID: 37005026 DOI: 10.1016/j.aca.2023.341116] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/13/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
Ag2O-Ag-porous silicon Bragg mirror (PSB) composite SERS substrates were successfully synthesized by using a combination of electrochemical and thermochemical methods. Test results showed that the SERS signal increased and decreased as the annealing temperature used for the substrate increased, where the most intense SERS signal was obtained using a substrate annealed at 300 °C. Stability test results showed substantial enhancement of the SERS signal intensity of the Ag2O-Ag-PSB composite one month after preparation compared with that of conventional Ag-PSB. We conclude that Ag2O nanoshells play an essential role in SERS signal enhancement. Ag2O prevents natural oxidation of Ag nanoparticles (AgNPs) and has a solid localized surface plasmon resonance (LSPR). SERS signal enhancement was tested using this substrate for serum from patients with Sjögren's syndrome (SS) and Diabetic nephropathy (DN), as well as from healthy controls (HC). SERS feature extraction was performed using principal component analysis (PCA). The extracted features were analyzed by a support vector machine (SVM) algorithm. Finally, a rapid screening model for SS and HC, as well as DN and HC, was developed and used to perform controlled experiments. The results showed that the diagnostic accuracy, sensitivity and selectivity for SERS technology combined with machine learning algorithms reached 90.7%, 93.4% and 86.7% for SS/HC and 89.3%, 95.6% and 80% for DN/HC, respectively. The results of this study show that the composite substrate has excellent potential to be developed into a commercially available SERS chip for medical testing.
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15
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Anand BG, Shejale KP, Rajesh Kumar R, Thangam R, Prajapati KP, Kar K, Mala R. Bioactivation of an orthodontic wire using multifunctional nanomaterials to prevent plaque accumulation. Biomater Adv 2023; 148:213346. [PMID: 36963344 DOI: 10.1016/j.bioadv.2023.213346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 01/29/2023] [Accepted: 02/12/2023] [Indexed: 02/18/2023]
Abstract
Controlling the growth of biofilm on orthodontic material has become a difficult challenge in modern dentistry. The antibacterial efficacy of currently used orthodontic material becomes limited due to the higher affinity of oral microbial flora for plaque formation on the material surface. Thus it is crutial to device an efficient strategy to prevent plaque buildup caused by pathogenic microbiota. In this work, we have fabricated a bioactive orthodontic wire using titanium nanoparticles (TiO2NPs) and silver nanoparticles (AgNPs). AgNPs were synthesized from the extracts of Ocimum sanctum, Ocimum tenuiflorum, Solanum surattense, and Syzygium aromaticum, while the TiO2NPs were synthesized by the Sol-Gel method. The nanoparticles were characterized by various biophysical techniques. The surface of the dental wire was molded by functionalizing these AgNPs followed by an additional coating of TiO2NPs. Functionalized dental wires were found to counteract the formation of tenacious intraoral biofilm, and showed an enhanced anti-bacterial effect against Multi-Drug Resistant (MDR) bacteria isolated from patients with various dental ailments. Data revealed that such surface coating counteracts the bacterial pathogens by inducing the leakage of Ag ions which eventually disrupts the cell membrane as confirmed from TEM micrographs. The results offer a significant opportunity for innovations in developing nanoparticle-based formulations to modify or fabricate an effective orthodontic material.
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Affiliation(s)
- Bibin G Anand
- Biomolecular Self Assembly Lab, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, Tamil Nadu-603203, India; Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110067, India.
| | - Kiran P Shejale
- Department of Chemical Engineering, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - R Rajesh Kumar
- School of Nanoscience and Technology, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Ramar Thangam
- Dynamic Nano-Bioengineering Lab, Department of Materials Science & Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Kailash Prasad Prajapati
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110067, India
| | - Karunakar Kar
- Biophysical and Biomaterials Research Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi- 110067, India
| | - R Mala
- Department of Biotechnology, Mepco Schlenk Engineering College, Sivakasi 626123, India.
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16
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Yu T, Jadhav AC, Xu J, Harris AL, Nair V, Huang WE. Metabolic Reprogramming in Colon Cancer Cells Persistently Infected with Newcastle Disease Virus. Cancers (Basel) 2023; 15. [PMID: 36765769 DOI: 10.3390/cancers15030811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Newcastle disease virus (NDV) is an oncolytic agent against various types of mammalian cancers. As with all cancer therapies, the development of cancer resistance, both innate and acquired, is becoming a challenge. In this study, we investigated persistently NDV-infected Caco-2 colon cancer cells, designated as virus-resistant (VR) Caco-2 cells, which were then able to resist NDV-mediated oncolysis. We applied single-cell Raman spectroscopy, combined with deuterium isotope probing (Raman-DIP) techniques, to investigate the metabolic adaptations and dynamics in VR Caco-2 cells. A linear discriminant analysis (LDA) model demonstrated excellent performance in differentiating VR Caco-2 from Caco-2 cells at single-cell level. By comparing the metabolic profiles in a time-resolved manner, the de novo synthesis of proteins and lipids was found upregulated, along with decreased DNA synthesis in VR Caco-2. The results suggest that VR Caco-2 cells might reprogram their metabolism and divert energy from proliferation to protein synthesis and lipidic modulation. The ability to identify and characterise single resistant cells among a population of cancer cells would help develop a deeper understanding of the resistance mechanisms and better tactics for developing effective cancer treatment.
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17
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Wang J, Meng S, Lin K, Yi X, Sun Y, Xu X, He N, Zhang Z, Hu H, Qie X, Zhang D, Tang Y, Huang WE, He J, Song Y. Leveraging single-cell Raman spectroscopy and single-cell sorting for the detection and identification of yeast infections. Anal Chim Acta 2023; 1239:340658. [PMID: 36628751 DOI: 10.1016/j.aca.2022.340658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/21/2022] [Indexed: 11/26/2022]
Abstract
Invasive fungal infection serves as a great threat to human health. Discrimination between fungal and bacterial infections at the earliest stage is vital for effective clinic practice; however, traditional culture-dependent microscopic diagnosis of fungal infection usually requires several days, meanwhile, culture-independent immunological and molecular methods are limited by the detectable type of pathogens and the issues with high false-positive rates. In this study, we proposed a novel culture-independent phenotyping method based on single-cell Raman spectroscopy for the rapid discrimination between fungal and bacterial infections. Three Raman biomarkers, including cytochrome c, peptidoglycan, and nucleic acid, were identified through hierarchical clustering analysis of Raman spectra across 12 types of most common yeast and bacterial pathogens. Compared to those of bacterial pathogens, the single cells of yeast pathogens demonstrated significantly stronger Raman peaks for cytochrome c, but weaker signals for peptidoglycan and nucleic acid. A two-step protocol combining the three biomarkers was established and able to differentiate fungal infections from bacterial infections with an overall accuracy of 94.9%. Our approach was also used to detect ten raw urinary tract infection samples. Successful identification of fungi was achieved within half an hour after sample obtainment. We further demonstrated the accurate fungal species taxonomy achieved with Raman-assisted cell ejection. Our findings demonstrate that Raman-based fungal identification is a novel, facile, reliable, and with a breadth of coverage approach, that has a great potential to be adopted in routine clinical practice to reduce the turn-around time of invasive fungal disease (IFD) diagnostics.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yixiang Sun
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, 20040, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Na He
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Zhiqiang Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Huijie Hu
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China
| | - Xingwang Qie
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Dayi Zhang
- College of New Energy and Environment, Jilin University, Changchun, 130021, PR China
| | - Yuguo Tang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China; Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, 215163, China.
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18
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Urbanczyk M, Jeyagaran A, Zbinden A, Lu CE, Marzi J, Kuhlburger L, Nahnsen S, Layland SL, Duffy G, Schenke-Layland K. Decorin improves human pancreatic β-cell function and regulates ECM expression in vitro. Matrix Biol 2023; 115:160-183. [PMID: 36592738 DOI: 10.1016/j.matbio.2022.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/23/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Transplantation of islets of Langerhans is a promising alternative treatment strategy in severe cases of type 1 diabetes mellitus; however, the success rate is limited by the survival rate of the cells post-transplantation. Restoration of the native pancreatic niche during transplantation potentially can help to improve cell viability and function. Here, we assessed for the first time the regulatory role of the small leucine-rich proteoglycan decorin (DCN) in insulin secretion in human β-cells, and its impact on pancreatic extracellular matrix (ECM) protein expression in vitro. In depth analyses utilizing next-generation sequencing as well as Raman microspectroscopy and Raman imaging identified pathways related to glucose metabolism to be upregulated in DCN-treated cells, including oxidative phosphorylation within the mitochondria as well as proteins and lipids of the endoplasmic reticulum. We further showed the effectiveness of DCN in a transplantation setting by treating collagen type 1-encapsulated β-cell-containing pseudo-islets with DCN. Taken together, in this study, we demonstrate the potential of DCN to improve the function of insulin-secreting β-cells while reducing the expression of ECM proteins affiliated with fibrotic capsule formation, making DCN a highly promising therapeutic agent for islet transplantation.
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Affiliation(s)
- Max Urbanczyk
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany
| | - Abiramy Jeyagaran
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Aline Zbinden
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany; Department of Immunology, Leiden University Medical Center Leiden, ZA 2333, the Netherlands
| | - Chuan-En Lu
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany
| | - Julia Marzi
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tübingen, Tübingen, Germany
| | - Laurence Kuhlburger
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany; Biomedical Data Science, Department of Computer Science, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany; Biomedical Data Science, Department of Computer Science, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Shannon L Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany; Department of Women's Health, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Garry Duffy
- Discipline of Anatomy and the Regenerative Medicine Institute, School of Medicine, College of Medicine Nursing and Health Sciences, National University of Ireland Galway, Ireland; Science Foundation Ireland (SFI) Centre for Research in Advanced Materials for Biomedical Engineering (AMBER), Trinity College Dublin & National University of Ireland Galway, Galway, Ireland
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, Silcherstr. 7/1, Tübingen 72076, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University Tübingen, Tübingen, Germany.
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19
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Cardoso-Lima R, Filho JFSD, de Araujo Dorneles ML, Gaspar RS, Souza PFN, Costa Dos Santos C, Santoro Rosa D, Santos-Oliveira R, Alencar LMR. Nanomechanical and Vibrational Signature of Chikungunya Viral Particles. Viruses 2022; 14. [PMID: 36560825 DOI: 10.3390/v14122821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Chikungunya virus (CHIKV) belongs to the genus Alphaviridae, with a single-stranded positive-sense RNA genome of 11.8 kbp encoding a polyprotein that generates both non-structural proteins and structural proteins. The virus is transmitted by the Aedes aegypti and A. albopictus mosquitoes, depending on the location. CHIKV infection leads to dengue-like musculoskeletal symptoms and has been responsible for several outbreaks worldwide since its discovery in 1952. Patients often experience fever, headache, muscle pain, joint swelling, and skin rashes. However, the ultrastructural and mechanical properties of CHIKV have not been fully characterized. Thus, this study aims to apply a physical approach to investigate CHIKV's ultrastructural morphology and mechanical properties, using atomic force microscopy and Raman spectroscopy as the main tools. Using nanomechanical assays of AFM and a gold nanoparticles substrate for Raman signal enhancement, we explored the conformational plasticity, morphology, vibrational signature, and nanomechanical properties of the chikungunya virus, providing new information on its ultrastructure at the nanoscale and offering a novel understanding of the virus' behavior upon mechanical disruptions besides its molecular composition.
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20
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Callery EL, Morais CLM, Nugent L, Rowbottom AW. Classification of Systemic Lupus Erythematosus Using Raman Spectroscopy of Blood and Automated Computational Detection Methods: A Novel Tool for Future Diagnostic Testing. Diagnostics (Basel) 2022; 12:diagnostics12123158. [PMID: 36553165 PMCID: PMC9777204 DOI: 10.3390/diagnostics12123158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to explore the proof of concept for using Raman spectroscopy as a diagnostic platform in the setting of systemic lupus erythematosus (SLE). We sought to identify unique Raman signatures in serum blood samples to successfully segregate SLE patients from healthy controls (HC). In addition, a retrospective audit was undertaken to assess the clinical utility of current testing platforms used to detect anti-double stranded DNA (dsDNA) antibodies (n = 600). We examined 234 Raman spectra to investigate key variances between SLE patients (n = 8) and HC (n = 4). Multi-variant analysis and classification model construction was achieved using principal component analysis (PCA), PCA-linear discriminant analysis and partial least squares-discriminant analysis (PLS-DA). We achieved the successful segregation of Raman spectra from SLE patients and healthy controls (p-value < 0.0001). Classification models built using PLS-DA demonstrated outstanding performance characteristics with 99% accuracy, 100% sensitivity and 99% specificity. Twelve statistically significant (p-value < 0.001) wavenumbers were identified as potential diagnostic spectral markers. Molecular assignments related to proteins and DNA demonstrated significant Raman intensity changes between SLE and HC groups. These wavenumbers may serve as future biomarkers and offer further insight into the pathogenesis of SLE. Our audit confirmed previously reported inconsistencies between two key methodologies used to detect anti-dsDNA, highlighting the need for improved laboratory testing for SLE. Raman spectroscopy has demonstrated powerful performance characteristics in this proof-of-concept study, setting the foundations for future translation into the clinical setting.
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Affiliation(s)
- Emma L. Callery
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- Correspondence: (E.L.C.); (A.W.R.)
| | - Camilo L. M. Morais
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
| | - Lucy Nugent
- Department of Immunology, Whiston Hospital, Prescot L35 5DR, UK
| | - Anthony W. Rowbottom
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- School of Medicine, University of Central Lancashire, Preston PR1 2HE, UK
- Correspondence: (E.L.C.); (A.W.R.)
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21
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Akram M, Majeed MI, Nawaz H, Rashid N, Javed MR, Ali MZ, Raza A, Shakeel M, Hasan HMU, Ali Z, Ehsan U, Shahid M. Surface-enhanced Raman spectroscopy for characterization of filtrate portions of blood serum samples of typhoid patients. Photodiagnosis Photodyn Ther 2022; 40:103199. [PMID: 36371020 DOI: 10.1016/j.pdpdt.2022.103199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Surface-enhanced Raman spectroscopy (SERS) is explored to design a rapid screening method for the characterization and diagnosis of typhoid fever by employing filtrate fractions of blood serum samples obtained by centrifugal filtration with 50 KDa filters. OBJECTIVES The purpose of this study, to separate the filtrate portions of blood serum samples in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire the SERS spectral features of smaller proteins more effectively which are probably associated with typhoid disease. Disease caused by Salmonella typhi diagnose more effectively by using surface-enhanced Raman spectroscopy (SERS) and multivariate data analysis tools. METHODS SERS was used as a diagnostic tool for typhoid fever by comparison between healthy and diseased samples. For this purpose, all the samples were analyzed by comparing their SERS spectral features. Over the spectral range of 400-1800cm-1, multivariate data analysis techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) are applied to diagnose and differentiate different filtrate fractions of blood serum samples of patients of typhoid fever and healthy ones. RESULTS By comparing SERS spectra of healthy filtrate with that of filtrate of typhoid sample, the SERS spectral features associated with disease development are identified including PCA is found to be efficient for the qualitative differentiation of all of the samples analyzed. Moreover, PLS-DA successfully identified and classified healthy and typhoid positive blood serum samples with 97 % accuracy, 99 % specificity, 91 % sensitivity and 0.78 area under the receiver operating characteristic (AUROC) curve. CONCLUSIONS Surface enhanced Raman spectroscopy using silver nanoparticles SERS substrate, is found to be useful technique for the quick identification and evaluation of filtrate fractions of the blood serum samples of healthy and typhoid samples for disease diagnosis.
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Affiliation(s)
- Maria Akram
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Muhammad Zeeshan Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ali Raza
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Hafiz Mahmood Ul Hasan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Zain Ali
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Usama Ehsan
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Shahid
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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22
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Milligan K, Van Nest SJ, Deng X, Ali-Adeeb R, Shreeves P, Punch S, Costie N, Pavey N, Crook JM, Berman DM, Brolo AG, Lum JJ, Andrews JL, Jirasek A. Raman spectroscopy and supervised learning as a potential tool to identify high-dose-rate-brachytherapy induced biochemical profiles of prostate cancer. J Biophotonics 2022; 15:e202200121. [PMID: 35908273 DOI: 10.1002/jbio.202200121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/14/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
High-dose-rate-brachytherapy (HDR-BT) is an increasingly attractive alternative to external beam radiation-therapy for patients with intermediate risk prostate cancer. Despite this, no bio-marker based method currently exists to monitor treatment response, and the changes which take place at the biochemical level in hypo-fractionated HDR-BT remain poorly understood. The aim of this pilot study is to assess the capability of Raman spectroscopy (RS) combined with principal component analysis (PCA) and random-forest classification (RF) to identify radiation response profiles after a single dose of 13.5 Gy in a cohort of nine patients. We here demonstrate, as a proof-of-concept, how RS-PCA-RF could be utilised as an effective tool in radiation response monitoring, specifically assessing the importance of low variance PCs in complex sample sets. As RS provides information on the biochemical composition of tissue samples, this technique could provide insight into the changes which take place on the biochemical level, as result of HDR-BT treatment.
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Affiliation(s)
- Kirsty Milligan
- Department of Physics, University of British Columbia, Kelowna, Canada
| | - Samantha J Van Nest
- Trev and Joyce Deeley Research Centre, BC Cancer-Victoria, Victoria, Canada
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York, USA
| | - Xinchen Deng
- Department of Physics, University of British Columbia, Kelowna, Canada
| | - Ramie Ali-Adeeb
- Department of Physics, University of British Columbia, Kelowna, Canada
| | - Phillip Shreeves
- Department of Mathematics and Statistics, University of British Columbia, Kelowna, Canada
| | - Samantha Punch
- Trev and Joyce Deeley Research Centre, BC Cancer-Victoria, Victoria, Canada
| | - Nathalie Costie
- Trev and Joyce Deeley Research Centre, BC Cancer-Victoria, Victoria, Canada
| | - Nils Pavey
- Trev and Joyce Deeley Research Centre, BC Cancer-Victoria, Victoria, Canada
| | - Juanita M Crook
- Sindi Ahluwalia Hawkins Centre for the Southern Interior, BC Cancer, Kelowna, Canada
- Department of Radiation Oncology, University of British Columbia, Kelowna, Canada
| | - David M Berman
- Department of Pathology and Molecular Medicine, Queens University, Kingston, Canada
| | | | - Julian J Lum
- Trev and Joyce Deeley Research Centre, BC Cancer-Victoria, Victoria, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Jeffrey L Andrews
- Department of Mathematics and Statistics, University of British Columbia, Kelowna, Canada
| | - Andrew Jirasek
- Department of Physics, University of British Columbia, Kelowna, Canada
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23
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Cao D, Lin H, Liu Z, Gu Y, Hua W, Cao X, Qian Y, Xu H, Zhu X. Serum-based surface-enhanced Raman spectroscopy combined with PCA-RCKNCN for rapid and accurate identification of lung cancer. Anal Chim Acta 2022; 1236:340574. [DOI: 10.1016/j.aca.2022.340574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/15/2022] [Accepted: 10/29/2022] [Indexed: 11/05/2022]
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24
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Hu H, Wang J, Yi X, Lin K, Meng S, Zhang X, Jiang C, Tang Y, Wang M, He J, Xu X, Song Y. Stain-free Gram staining classification of pathogens via single-cell Raman spectroscopy combined with machine learning. Anal Methods 2022; 14:4014-4020. [PMID: 36196964 DOI: 10.1039/d2ay01056a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Gram staining (GS) is one of the routine microbiological operations to classify bacteria based on the cell wall structure. Accurate GS classification of pathogens is of great significance since it helps correct administration of antimicrobial treatment. The laborious procedure and low sensitivity results related to conventional GS have resulted in reluctance among clinicians. In this study, we integrate confocal Raman spectroscopy and machine learning techniques to distinguish Gram-negative (GN) or Gram-positive (GP) bacteria. A single-cell Raman database including seven most common clinical pathogens (three GP strains and four GN strains) was constructed. Machine learning algorithms including the support-vector machine (SVM), k-nearest neighbors' algorithm (k-NN), gradient boosting machine (GBM), linear discriminant analysis (LDA), and t-distributed stochastic neighbor embedding (t-SNE) were trained to achieve the binary classification for GS. With such a relatively small database, the SVM model achieved the highest accuracy of 98.1%. The molecular signatures of GN and GP embedded in their Raman fingerprints were identified with hierarchical cluster analysis (HCA). The results indicated that Raman peaks for peptidoglycan and teichoic acid were the most significant factors that contributed to accurate classification. The Raman machine learning approach could greatly enhance the diagnosis of pathogenic infections.
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Affiliation(s)
- Huijie Hu
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xiaofei Yi
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Kaicheng Lin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Xin Zhang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Chongqing Guoke Medical Technology Development Co., Ltd, Chongqing 400799, PR China
| | - Chenyu Jiang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
- Jinan Guoke Medical Technology Development Co., Ltd, Jinan 250102, PR China
| | - Yuguo Tang
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Jian He
- State Key Laboratory of Oncogenes and Related Genes, Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, PR China.
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai 200040, PR China.
| | - Yizhi Song
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou 215163, PR China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, PR China.
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25
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Mushtaq A, Nawaz H, Irfan Majeed M, Rashid N, Tahir M, Zaman Nawaz M, Shahzad K, Dastgir G, Zaki Abdul Bari R, Ul Haq A, Saleem M, Akhtar F. Surface-enhanced Raman spectroscopy (SERS) for monitoring colistin-resistant and susceptible E. coli strains. Spectrochim Acta A Mol Biomol Spectrosc 2022; 278:121315. [PMID: 35576839 DOI: 10.1016/j.saa.2022.121315] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/21/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Abstract
The emergence of drug-resistant bacteria is a precarious global health concern. In this study, surface-enhanced Raman spectroscopy (SERS) is used to characterize colistin-resistant and susceptible E. coli strains based on their distinguished SERS spectral features for the development of rapid and cost-effective detection and differentiation methods. For this purpose, three colistin-resistant and three colistin susceptible E. coli strains were analyzed by comparing their SERS spectral signatures. Moreover, multivariate data analysis techniques including Principal component analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) were used to examine the SERS spectral data of colistin-resistant and susceptible strains. PCA technique was employed for differentiating colistin susceptible and resistant E.coli strains due to alteration in biochemical compositions of the bacterial cell. PLS-DA is employed on SERS spectral data sets for discrimination of these resistant and susceptible E. coli strains with 100% specificity, 100% accuracy, 99.8% sensitivity, and 86% area under receiver operating characteristics (AUROC) curve.
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Affiliation(s)
- Aqsa Mushtaq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Tahir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Muhammad Zaman Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Kashif Shahzad
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Ghulam Dastgir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Rana Zaki Abdul Bari
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Anwar Ul Haq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Mudassar Saleem
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Farwa Akhtar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
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26
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Wu J, Cui X, Kang Z, Wang S, Zhu G, Yang S, Wang S, Li H, Lu C, Lv X. Rapid diagnosis of diabetes based on ResNet and Raman spectroscopy. Photodiagnosis Photodyn Ther 2022; 39:103007. [PMID: 35817371 DOI: 10.1016/j.pdpdt.2022.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 10/17/2022]
Abstract
Diabetes mellitus is a global public health problem, and the epidemic situation in China is particularly serious. The prevalence of the disease has been increasing in recent years, and the number of patients is the highest in the world. Diabetes has become another chronic non-communicable disease that seriously endangers the health of our people after cardiovascular and cerebrovascular diseases and tumors. In this study, urine sample data were collected from 37 diabetic patients and 37 healthy volunteers using Raman spectroscopy. The collected data were preprocessed using an adaptive iterative reweighted penalized least squares (airPLS) algorithm and a polynomial Savitzky-Golay smoothing algorithm. After extracting features using principal component analysis (PCA) dimensionality reduction algorithm, ResNet, support vector machine (SVM) and linear discriminant analysis (LDA) classification models were selected to classify and identify diabetic patients and healthy controls. The results show that ResNet has the best discrimination effect, and the average accuracy, recall and F1-score can reach 84.28%, 86.20% and 84.02% respectively after five cross-validations, and the area under the subject working characteristic (ROC) curve is 0.93. The experimental results show that the model established in this paper is simple to operate, highly accurate and has good reference value for rapid screening of diabetes.
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Affiliation(s)
- Jianying Wu
- Xinjiang Key Laboratory for Luminescence Minerals and Optical Functional Materials, School of Physics and Electronic Engineering, Xinjiang Normal University, Urumqi, Xinjiang 830054, China
| | - Xinyue Cui
- Shihezi University, Shihezi, Xinjiang 832003, China
| | - Zhenping Kang
- College of Information Science and Engineering, Xinjiang University, Urumqi, Xinjiang 830046, China
| | - Shanshan Wang
- Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Guoqiang Zhu
- Xinjiang Medical University, Urumqi, Xinjiang 830054, China
| | - Shufen Yang
- Department of Nephrology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830001, China
| | - Shun Wang
- Department of Nephrology, People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi, Xinjiang 830001, China
| | - Hongtao Li
- Xinjiang Medical University Affiliated Tumor Hospital, Urumqi, Xinjiang 830011, China
| | - Chen Lu
- Department of Nephrology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China.
| | - Xiaoyi Lv
- College of Software, Xinjiang University, Urumqi, Xinjiang 830046, China.
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27
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Cui D, Kong L, Wang Y, Zhu Y, Zhang C. In situ identification of environmental microorganisms with Raman spectroscopy. Environ Sci Ecotechnol 2022; 11:100187. [PMID: 36158754 PMCID: PMC9488013 DOI: 10.1016/j.ese.2022.100187] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 05/28/2023]
Abstract
Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.
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Affiliation(s)
- Dongyu Cui
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yi Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, University of Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
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Becker L, Fischer F, Fleck JL, Harland N, Herkommer A, Stenzl A, Aicher WK, Schenke-Layland K, Marzi J. Data-Driven Identification of Biomarkers for In Situ Monitoring of Drug Treatment in Bladder Cancer Organoids. Int J Mol Sci 2022; 23:ijms23136956. [PMID: 35805961 PMCID: PMC9266781 DOI: 10.3390/ijms23136956] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 02/01/2023] Open
Abstract
Three-dimensional (3D) organoid culture recapitulating patient-specific histopathological and molecular diversity offers great promise for precision medicine in cancer. In this study, we established label-free imaging procedures, including Raman microspectroscopy (RMS) and fluorescence lifetime imaging microscopy (FLIM), for in situ cellular analysis and metabolic monitoring of drug treatment efficacy. Primary tumor and urine specimens were utilized to generate bladder cancer organoids, which were further treated with various concentrations of pharmaceutical agents relevant for the treatment of bladder cancer (i.e., cisplatin, venetoclax). Direct cellular response upon drug treatment was monitored by RMS. Raman spectra of treated and untreated bladder cancer organoids were compared using multivariate data analysis to monitor the impact of drugs on subcellular structures such as nuclei and mitochondria based on shifts and intensity changes of specific molecular vibrations. The effects of different drugs on cell metabolism were assessed by the local autofluorophore environment of NADH and FAD, determined by multiexponential fitting of lifetime decays. Data-driven neural network and data validation analyses (k-means clustering) were performed to retrieve additional and non-biased biomarkers for the classification of drug-specific responsiveness. Together, FLIM and RMS allowed for non-invasive and molecular-sensitive monitoring of tumor-drug interactions, providing the potential to determine and optimize patient-specific treatment efficacy.
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Affiliation(s)
- Lucas Becker
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, 72076 Tuebingen, Germany; (L.B.); (K.S.-L.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
| | - Felix Fischer
- Institute of Applied Optics (ITO), University of Stuttgart, 70569 Stuttgart, Germany; (F.F.); (A.H.)
| | - Julia L. Fleck
- Mines Saint-Etienne, CNRS, UMR 6158 LIMOS, Centre CIS, Université Clermont Auvergne, 42270 Saint Jarez-en-Priest, France;
| | - Niklas Harland
- Department of Urology, University of Tuebingen Hospital, 72076 Tuebingen, Germany; (N.H.); (A.S.)
| | - Alois Herkommer
- Institute of Applied Optics (ITO), University of Stuttgart, 70569 Stuttgart, Germany; (F.F.); (A.H.)
| | - Arnulf Stenzl
- Department of Urology, University of Tuebingen Hospital, 72076 Tuebingen, Germany; (N.H.); (A.S.)
| | - Wilhelm K. Aicher
- Center of Medical Research, Department of Urology at UKT, University of Tuebingen, 72076 Tuebingen, Germany;
| | - Katja Schenke-Layland
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, 72076 Tuebingen, Germany; (L.B.); (K.S.-L.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tueingen, 72770 Reutlingen, Germany
| | - Julia Marzi
- Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, 72076 Tuebingen, Germany; (L.B.); (K.S.-L.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tuebingen, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tueingen, 72770 Reutlingen, Germany
- Correspondence:
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Shakeel S, Nawaz H, Majeed MI, Rashid N, Javed MR, Tariq A, Majeed B, Sehar A, Murtaza S, Sadaf N, Rimsha G, Amin I. Surface-enhanced Raman spectroscopic analysis of the centrifugally filtered blood serum samples of the hepatitis C patients. Photodiagnosis Photodyn Ther 2022; 39:102949. [PMID: 35661826 DOI: 10.1016/j.pdpdt.2022.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Previously Raman spectroscopy technique is a use to analyze non-invasive disease related to body fluids. OBJECTIVES For the qualitative and quantitative analysis of HCV serum samples surface-enhanced Raman spectroscopy (SERS) based method is developed. METHOD Surface-enhanced Raman spectroscopy (SERS) technique is employed for analysis of filtrate portions of blood serum samples of hepatitis C virus (HCV) infected patients and healthy ones by using 50 kDa centrifugal filter device. The filtrate portions of the serum obtained in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire SERS spectral features of smaller proteins more effectively which are probably associated with Hepatitis C infection. Moreover, SERS spectral features of the filtrates of different level of viral load including low, medium and high viral loads are compared with SERS spectral features of the filtrate portions of healthy/control serum samples. SERS spectral data sets of different samples are further analyzed by using multivariate data analysis techniques such as principal component analysis (PCA) and partial least square regression (PLSR). Some SERS spectral features are solely observed in the filtrate portions of the serum samples of hepatitis C and their intensities are increased as the level of viral load increases and might be used for HCV diagnosis. RESULTS PCA was found helpful for differentiation of SERS spectral data sets of filtrate portions of the serum samples of hepatitis C and healthy persons. The PLSR model helped for the quantification of viral loads in the unknown serum samples with 99 % accuracy.
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Affiliation(s)
- Samra Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Muhammad Irfan Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan.
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad Campus, Faisalabad 38000, Pakistan.
| | - Muhammad Rizwan Javed
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad 38000, Pakistan
| | - Ayesha Tariq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Beenish Majeed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Aafia Sehar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Sania Murtaza
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Nimra Sadaf
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Gull Rimsha
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan
| | - Imran Amin
- PCR Laboratory, PINUM Hospital, Faisalabad 38000, Pakistan
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Parlatan U, Parlatan S, Sen K, Kecoglu I, Ulukan MO, Karakaya A, Erkanli K, Turkoglu H, Ugurlucan M, Unlu MB, Tanoren B. Atrial fibrillation designation with micro-Raman spectroscopy and scanning acoustic microscope. Sci Rep 2022; 12:6461. [PMID: 35440791 PMCID: PMC9018680 DOI: 10.1038/s41598-022-10380-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Atrial fibrillation (AF) is diagnosed with the electrocardiogram, which is the gold standard in clinics. However, sufficient arrhythmia monitoring takes a long time, and many of the tests are made in only a few seconds, which can lead arrhythmia to be missed. Here, we propose a combined method to detect the effects of AF on atrial tissue. We characterize tissues obtained from patients with or without AF by scanning acoustic microscopy (SAM) and by Raman spectroscopy (RS) to construct a mechano-chemical profile. We classify the Raman spectral measurements of the tissue samples with an unsupervised clustering method, k-means and compare their chemical properties. Besides, we utilize scanning acoustic microscopy to compare and determine differences in acoustic impedance maps of the groups. We compared the clinical outcomes with our findings using a neural network classification for Raman measurements and ANOVA for SAM measurements. Consequently, we show that the stiffness profiles of the tissues, corresponding to the patients with chronic AF, without AF or who experienced postoperative AF, are in agreement with the lipid-collagen profiles obtained by the Raman spectral characterization.
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Affiliation(s)
- Ugur Parlatan
- Department of Physics, Bogazici University, Istanbul, 34342, Turkey.
| | - Seyma Parlatan
- Vocational School of Health Services, Istinye University, Istanbul, 34020, Turkey
| | - Kubra Sen
- Department of Physics, Bogazici University, Istanbul, 34342, Turkey
| | - Ibrahim Kecoglu
- Department of Physics, Bogazici University, Istanbul, 34342, Turkey
| | - Mustafa Ozer Ulukan
- Department of Cardiovascular Surgery, Istanbul Medipol University, Istanbul, 34214, Turkey
| | - Atalay Karakaya
- Department of Cardiovascular Surgery, Istanbul Medipol University, Istanbul, 34214, Turkey
| | - Korhan Erkanli
- Department of Cardiovascular Surgery, Istanbul Medipol University, Istanbul, 34214, Turkey
| | - Halil Turkoglu
- Department of Cardiovascular Surgery, Istanbul Medipol University, Istanbul, 34214, Turkey
| | - Murat Ugurlucan
- Department of Cardiovascular Surgery, Istanbul Medipol University, Istanbul, 34214, Turkey
| | - Mehmet Burcin Unlu
- Department of Physics, Bogazici University, Istanbul, 34342, Turkey.,Global Station for Quantum Medical Science and Engineering, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Bukem Tanoren
- Department of Natural Sciences, Acıbadem University, Istanbul, 34684, Turkey
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31
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Holl M, Rasch ML, Becker L, Keller AL, Schultze-Rhonhof L, Ruoff F, Templin M, Keller S, Neis F, Keßler F, Andress J, Bachmann C, Krämer B, Schenke-Layland K, Brucker SY, Marzi J, Weiss M. Cell Type-Specific Anti-Adhesion Properties of Peritoneal Cell Treatment with Plasma-Activated Media (PAM). Biomedicines 2022; 10:biomedicines10040927. [PMID: 35453677 PMCID: PMC9032174 DOI: 10.3390/biomedicines10040927] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
Postoperative abdominal adhesions are responsible for serious clinical disorders. Administration of plasma-activated media (PAM) to cell type-specific modulated proliferation and protein biosynthesis is a promising therapeutic strategy to prevent pathological cell responses in the context of wound healing disorders. We analyzed PAM as a therapeutic option based on cell type-specific anti-adhesive responses. Primary human peritoneal fibroblasts and mesothelial cells were isolated, characterized and exposed to different PAM dosages. Cell type-specific PAM effects on different cell components were identified by contact- and marker-independent Raman imaging, followed by thorough validation by specific molecular biological methods. The investigation revealed cell type-specific molecular responses after PAM treatment, including significant cell growth retardation in peritoneal fibroblasts due to transient DNA damage, cell cycle arrest and apoptosis. We identified a therapeutic dose window wherein specifically pro-adhesive peritoneal fibroblasts were targeted, whereas peritoneal mesothelial cells retained their anti-adhesive potential of epithelial wound closure. Finally, we demonstrate that PAM treatment of peritoneal fibroblasts reduced the expression and secretion of pro-adhesive cytokines and extracellular matrix proteins. Altogether, we provide insights into biochemical PAM mechanisms which lead to cell type-specific pro-therapeutic cell responses. This may open the door for the prevention of pro-adhesive clinical disorders.
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Affiliation(s)
- Myriam Holl
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Marie-Lena Rasch
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Lucas Becker
- Institute of Biomedical Engineering, Eberhard Karls University Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72076 Tübingen, Germany
| | - Anna-Lena Keller
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Laura Schultze-Rhonhof
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Felix Ruoff
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Markus Templin
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Silke Keller
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
| | - Felix Neis
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Franziska Keßler
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Jürgen Andress
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Cornelia Bachmann
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Bernhard Krämer
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
- Institute of Biomedical Engineering, Eberhard Karls University Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72076 Tübingen, Germany
- Department of Medicine/Cardiology, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Sara Y. Brucker
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
| | - Julia Marzi
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
- Institute of Biomedical Engineering, Eberhard Karls University Tübingen, 72076 Tübingen, Germany;
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University, 72076 Tübingen, Germany
| | - Martin Weiss
- Department of Women’s Health Tübingen, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (M.H.); (M.-L.R.); (L.S.-R.); (F.N.); (F.K.); (J.A.); (C.B.); (B.K.); (S.Y.B.)
- NMI Natural and Medical Sciences Institute, University Tübingen, 72770 Reutlingen, Germany; (A.-L.K.); (F.R.); (M.T.); (S.K.); (K.S.-L.); (J.M.)
- Correspondence:
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Stevens AR, Stickland CA, Harris G, Ahmed Z, Goldberg Oppenheimer P, Belli A, Davies DJ. Raman Spectroscopy as a Neuromonitoring Tool in Traumatic Brain Injury: A Systematic Review and Clinical Perspectives. Cells 2022; 11:1227. [PMID: 35406790 PMCID: PMC8997459 DOI: 10.3390/cells11071227] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022] Open
Abstract
Traumatic brain injury (TBI) is a significant global health problem, for which no disease-modifying therapeutics are currently available to improve survival and outcomes. Current neuromonitoring modalities are unable to reflect the complex and changing pathophysiological processes of the acute changes that occur after TBI. Raman spectroscopy (RS) is a powerful, label-free, optical tool which can provide detailed biochemical data in vivo. A systematic review of the literature is presented of available evidence for the use of RS in TBI. Seven research studies met the inclusion/exclusion criteria with all studies being performed in pre-clinical models. None of the studies reported the in vivo application of RS, with spectral acquisition performed ex vivo and one performed in vitro. Four further studies were included that related to the use of RS in analogous brain injury models, and a further five utilised RS in ex vivo biofluid studies for diagnosis or monitoring of TBI. RS is identified as a potential means to identify injury severity and metabolic dysfunction which may hold translational value. In relation to the available evidence, the translational potentials and barriers are discussed. This systematic review supports the further translational development of RS in TBI to fully ascertain its potential for enhancing patient care.
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Affiliation(s)
- Andrew R. Stevens
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
| | - Clarissa A. Stickland
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Georgia Harris
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Zubair Ahmed
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Pola Goldberg Oppenheimer
- School of Chemical Engineering, University of Birmingham, Birmingham B15 2TT, UK; (C.A.S.); (G.H.); (P.G.O.)
| | - Antonio Belli
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
| | - David J. Davies
- Neuroscience, Trauma and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK; (Z.A.); (A.B.); (D.J.D.)
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospitals Birmingham, Birmingham B15 2TH, UK
- Centre for Trauma Science Research, University of Birmingham, Birmingham B15 2TT, UK
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Jaafar A, Holomb R, Sdobnov AY, Ocskay Z, Jakus Z, Tuchin VV, Veres M. Ex vivo confocal Raman microspectroscopy of porcine dura mater supported by optical clearing. J Biophotonics 2022; 15:e202100332. [PMID: 34951739 DOI: 10.1002/jbio.202100332] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
The effect of tissue optical clearing (TOC) to increase the probing depth and observe in-depth structure of the ex vivo porcine dura mater was studied by confocal Raman microspectroscopy (CRM). Raman intensities were significantly increased at the depth of 250 μm for all collagen bands after treatment with glycerol. The influence of glycerol on collagen hydration was also investigated. The results indicate that the process of TOC can be divided into three main steps. The first one is a fast process of tissue dehydration accompanied by collagen shrinkage while the second relatively slow process is related to the glycerol penetration into the interfibrillar space of collagen combined with swelling of tissue. The third step is collagen dissociation caused by the high concentration of glycerol. To the best of our knowledge, this study is the first example to introduce the TOC technique in assisting CRM of ex vivo dura mater in-depth probing.
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Affiliation(s)
- Ali Jaafar
- Institute for Solid State Physics and Optics, Wigner Research Center for Physics, Budapest, Hungary
- Institute of Physics, University of Szeged, Szeged, Hungary
- Ministry of Higher Education and Scientific Research, Baghdad, Iraq
| | - Roman Holomb
- Institute for Solid State Physics and Optics, Wigner Research Center for Physics, Budapest, Hungary
- Department of Information Control Systems and Technologies, Uzhhorod National University, Uzhhorod, Ukraine
| | - Anton Y Sdobnov
- Science Medical Center, Saratov State University, Saratov, Russia
- Optoelectronics and Measurement Techniques Laboratory, University of Oulu, Oulu, Finland
| | - Zsombor Ocskay
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Zoltán Jakus
- Department of Physiology, Semmelweis University School of Medicine, Budapest, Hungary
| | - Valery V Tuchin
- Science Medical Center, Saratov State University, Saratov, Russia
- Laboratory of Laser Diagnostics of Technical and Living Systems, Institute of Precision Mechanics and Control of the Russian Academy of Sciences, Saratov, Russia
- А.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Miklós Veres
- Institute for Solid State Physics and Optics, Wigner Research Center for Physics, Budapest, Hungary
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Czaja M, Skirlińska-Nosek K, Adamczyk O, Sofińska K, Wilkosz N, Rajfur Z, Szymoński M, Lipiec E. Raman Research on Bleomycin-Induced DNA Strand Breaks and Repair Processes in Living Cells. Int J Mol Sci 2022; 23:3524. [PMID: 35408885 DOI: 10.3390/ijms23073524] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/20/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023] Open
Abstract
Even several thousands of DNA lesions are induced in one cell within one day. DNA damage may lead to mutations, formation of chromosomal aberrations, or cellular death. A particularly cytotoxic type of DNA damage is single- and double-strand breaks (SSBs and DSBs, respectively). In this work, we followed DNA conformational transitions induced by the disruption of DNA backbone. Conformational changes of chromatin in living cells were induced by a bleomycin (BLM), an anticancer drug, which generates SSBs and DSBs. Raman micro-spectroscopy enabled to observe chemical changes at the level of single cell and to collect hyperspectral images of molecular structure and composition with sub-micrometer resolution. We applied multivariate data analysis methods to extract key information from registered data, particularly to probe DNA conformational changes. Applied methodology enabled to track conformational transition from B-DNA to A-DNA upon cellular response to BLM treatment. Additionally, increased expression of proteins within the cell nucleus resulting from the activation of repair processes was demonstrated. The ongoing DNA repair process under the BLM action was also confirmed with confocal laser scanning fluorescent microscopy.
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35
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Talik Sisin NN, Abdul Razak K, Che Mat NF, Abdullah R, Ab Rashid R, Mohd Zainudin NH, Khairil Anuar MA, Jamil A, Geso M, Rahman WN. The effects of bismuth oxide nanoparticles and cisplatin on MCF-7 breast cancer cells irradiated with Ir-192 High Dose Rate brachytherapy. Journal of Radiation Research and Applied Sciences 2022; 15:159-71. [DOI: 10.1016/j.jrras.2022.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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36
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Yang X, Wu Z, Ou Q, Qian K, Jiang L, Yang W, Shi Y, Liu G. Diagnosis of Lung Cancer by FTIR Spectroscopy Combined With Raman Spectroscopy Based on Data Fusion and Wavelet Transform. Front Chem 2022; 10:810837. [PMID: 35155366 PMCID: PMC8825776 DOI: 10.3389/fchem.2022.810837] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Abstract
Lung cancer is a fatal tumor threatening human health. It is of great significance to explore a diagnostic method with wide application range, high specificity, and high sensitivity for the detection of lung cancer. In this study, data fusion and wavelet transform were used in combination with Fourier transform infrared (FTIR) spectroscopy and Raman spectroscopy to study the serum samples of patients with lung cancer and healthy people. The Raman spectra of serum samples can provide more biological information than the FTIR spectra of serum samples. After selecting the optimal wavelet parameters for wavelet threshold denoising (WTD) of spectral data, the partial least squares–discriminant analysis (PLS-DA) model showed 93.41% accuracy, 96.08% specificity, and 90% sensitivity for the fusion data processed by WTD in the prediction set. The results showed that the combination of FTIR spectroscopy and Raman spectroscopy based on data fusion and wavelet transform can effectively diagnose patients with lung cancer, and it is expected to be applied to clinical screening and diagnosis in the future.
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Affiliation(s)
- Xien Yang
- Yunnan Key Laboratory of Opto-electronic Information Technology, School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Zhongyu Wu
- Yunnan Key Laboratory of Opto-electronic Information Technology, School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Quanhong Ou
- Yunnan Key Laboratory of Opto-electronic Information Technology, School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Kai Qian
- Department of Thoracic Surgery, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Liqin Jiang
- Yunnan Key Laboratory of Opto-electronic Information Technology, School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Weiye Yang
- School of Preclinical Medicine, Zunyi Medical University, Zunyi, China
| | - Youming Shi
- School of Physics and Electronic Engineering, Qujing Normal University, Qujing, China
| | - Gang Liu
- Yunnan Key Laboratory of Opto-electronic Information Technology, School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
- *Correspondence: Gang Liu,
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37
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Pezzotti G, Zhu W, Terai Y, Marin E, Boschetto F, Kawamoto K, Itaka K. Raman spectroscopic insight into osteoarthritic cartilage regeneration by mRNA therapeutics encoding cartilage-anabolic transcription factor Runx1. Mater Today Bio 2022; 13:100210. [PMID: 35281370 PMCID: PMC8913780 DOI: 10.1016/j.mtbio.2022.100210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/18/2022] [Accepted: 01/28/2022] [Indexed: 11/05/2022] Open
Abstract
While joint arthroplasty remains nowadays the most popular option available to repair chronically degenerated osteoarthritic joints, possibilities are recently emerging for regeneration of damaged cartilage rather than its replacement with artificial biomaterials. This latter strategy could allow avoiding the quite intrusive surgical procedures associated with total joint replacement. Building upon this notion, we first apply Raman spectroscopy to characterize diseased cartilage in a mice model of instability-induced knee osteoarthritis (OA) upon medial collateral ligament (MCL) and medial meniscus (MM) transections. Then, we examine the same OA model after cartilage regeneration by means of messenger RNA (mRNA) delivery of a cartilage-anabolic runt-related transcription factor 1 (RUNX1). Raman spectroscopy is shown to substantiate at the molecular scale the therapeutic effect of the Runx1 mRNA cartilage regeneration approach. This study demonstrates how the Raman spectroscopic method could support and accelerate the development of new therapies for cartilage diseases.
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Akbar S, Majeed MI, Nawaz H, Rashid N, Tariq A, Hameed W, Shakeel S, Dastgir G, Bari RZA, Iqbal M, Nawaz A, Akram M. Surface-Enhanced Raman Spectroscopic (SERS) Characterization of Low Molecular Weight Fraction of the Serum of Breast Cancer Patients with Principal Component Analysis (PCA) and Partial Least Square-Discriminant Analysis (PLS-DA). ANAL LETT 2021. [DOI: 10.1080/00032719.2021.2017948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Saba Akbar
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Haq Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Nosheen Rashid
- Department of Chemistry, University of Education, Faisalabad, Pakistan
| | - Ayesha Tariq
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Wajeeha Hameed
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Samra Shakeel
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Ghulam Dastgir
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Rana Zaki Abdul Bari
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Maham Iqbal
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Amna Nawaz
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Maria Akram
- Department of Chemistry, University of Agriculture Faisalabad, Faisalabad, Pakistan
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Bonsignore M, Trusso S, De Pasquale C, Ferlazzo G, Allegra A, Innao V, Musolino C, Franco D, Maria De Plano L, Guglielmino SPP, Neri F, Fazio E. A multivariate analysis of Multiple Myeloma subtype plasma cells. Spectrochim Acta A Mol Biomol Spectrosc 2021; 258:119813. [PMID: 33892305 DOI: 10.1016/j.saa.2021.119813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/04/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Trusted methods for identifying different Multiple Myeloma (MM) cells and their biological diversity due to their immunophenotypic variety are often little detailed and difficult to find in literature. In this work, we show that micro-Raman spectroscopy can be used to highlight if there is a certain degree of distinction or correlation between the MM subtype plasmacells in relation to the cluster of differentiation (CD45+/CD38+/CD138-) and (CD45-/CD38+/CD138+). After taking samples from the bone marrow of patients with Multiple Myeloma, the PCs were sorted by flow cytometry, selecting the most common CD of the disease, i.e. CD 45, CD38 and CD138. Some spectral differences are observed comparing the Raman spectra of the two set of samples investigated. To better define in which spectral regions there are greater differences and, therefore, to which biological contributions the changes refers, we also explored the principal component analysis (PCA) of the collected Raman data. The spectral variations between the different sorted cells have been highlighted by plotting loading vectors PC1 and PC2, which shows a net differentiation between the two set of cells. Ultimately, the differences shown by PCA have been associated with the spectral variations observed and explained in terms of changes of proteins and lipid contributions. Thus, the differentiation of Multiple Myeloma subtype plasma cells by confocal micro-Raman spectroscopy can be proposed as a diagnostic tool in the speeding up of cell identification, assessing the intracellular biochemical changes that take place in cancer cells.
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Affiliation(s)
- Martina Bonsignore
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, University of Messina, Italy
| | - Sebastiano Trusso
- Institute of Chemical-Physical Processes (IPCF)-CNR, Messina, Italy.
| | - Claudia De Pasquale
- Laboratory of Immunology and Biotherapy, Department of Human Pathology, University of Messina, Italy
| | - Guido Ferlazzo
- Laboratory of Immunology and Biotherapy, Department of Human Pathology, University of Messina, Italy
| | - Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi" University of Messina, Italy
| | - Vanessa Innao
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi" University of Messina, Italy
| | - Caterina Musolino
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi" University of Messina, Italy
| | - Domenico Franco
- Department of Chemical Sciences, Biological, Pharmaceutical and Environmental, University of Messina, Italy
| | - Laura Maria De Plano
- Department of Chemical Sciences, Biological, Pharmaceutical and Environmental, University of Messina, Italy
| | | | - Fortunato Neri
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, University of Messina, Italy
| | - Enza Fazio
- Department of Mathematical and Computational Sciences, Physical Science and Earth Science, University of Messina, Italy.
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40
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Santos NR, Künzel R, Freitas MB, Levenhagen RS, Marques APDA, Courrol LC. Raman and Fluorescence Profiles Modifications of Muscular and Adipose Tissues Exposed to Low Energy X-ray Beams. Appl Spectrosc 2021; 75:1124-1135. [PMID: 33464152 DOI: 10.1177/0003702821989773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This work aims to investigate changes induced by low-energy radiation in adipose and muscular tissues employing autofluorescence and Raman spectroscopic techniques. X-ray beams expositions with 25 and 35 kV at 0.11, 1.1, and 2.1 Gy radiation dose levels were applied. Changes in Raman line intensities at specific bands assigned to collagen, proteins, and lipids were observed. Autofluorescent analysis exhibit variations in the collagen and nicotinamide adenine dinucleotide emission (NADH), resulting from the structural modifications, variations on the reduced/oxidized fluorophores equilibrium followed by radiation exposure. Results show that Raman and fluorescence spectroscopy are suitable techniques to evaluate radiation effects on biomolecules even at low radiation doses and energies.
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Affiliation(s)
- Noemy R Santos
- Departamento de Fisica, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
| | - Roseli Künzel
- Departamento de Fisica, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
| | - Marcelo B Freitas
- Departamento de Biofisica, Escola Paulista de Medicina, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
| | - Ronaldo S Levenhagen
- Departamento de Fisica, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
| | - Ana Paula de A Marques
- Departamento de Quimica, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
| | - Lilia C Courrol
- Departamento de Fisica, Universidade Federal de Sao Paulo-28105UNIFESP, Sao Paulo, Brazil
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41
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Ustaoglu SG, Ali MHM, Rakib F, Blezer ELA, Van Heijningen CL, Dijkhuizen RM, Severcan F. Biomolecular changes and subsequent time-dependent recovery in hippocampal tissue after experimental mild traumatic brain injury. Sci Rep 2021; 11:12468. [PMID: 34127773 PMCID: PMC8203626 DOI: 10.1038/s41598-021-92015-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022] Open
Abstract
Traumatic brain injury (TBI) is the main cause of disability and mortality in individuals under the age of 45 years. Elucidation of the molecular and structural alterations in brain tissue due to TBI is crucial to understand secondary and long-term effects after traumatic brain injury, and to develop and apply the correct therapies. In the current study, the molecular effects of TBI were investigated in rat brain at 24 h and 1 month after the injury to determine acute and chronic effects, respectively by Fourier transform infrared imaging. This study reports the time-dependent contextual and structural effects of TBI on hippocampal brain tissue. A mild form of TBI was induced in 11-week old male Sprague Dawley rats by weight drop. Band area and intensity ratios, band frequency and bandwidth values of specific spectral bands showed that TBI causes significant structural and contextual global changes including decrease in carbonyl content, unsaturated lipid content, lipid acyl chain length, membrane lipid order, total protein content, lipid/protein ratio, besides increase in membrane fluidity with an altered protein secondary structure and metabolic activity in hippocampus 24 h after injury. However, improvement and/or recovery effects in these parameters were observed at one month after TBI.
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Affiliation(s)
- Sebnem Garip Ustaoglu
- Department of Medical Biochemistry, Faculty of Medicine, Altinbas University, Bakirkoy, Istanbul, Turkey.
| | - Mohamed H M Ali
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110, Doha, Qatar.
| | - Fazle Rakib
- Department of Chemistry and Earth Sciences, Qatar University, Doha, Qatar
| | - Erwin L A Blezer
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline L Van Heijningen
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rick M Dijkhuizen
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altinbas University, Bakirkoy, Istanbul, Turkey.,Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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42
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Fu Y, Hu F, Li H, Cui L, Qian G, Zhang D, Xu Y. Application and mechanisms of microalgae harvesting by magnetic nanoparticles (MNPs). Sep Purif Technol 2021; 265:118519. [DOI: 10.1016/j.seppur.2021.118519] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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43
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K MG, Barzegari S, Hajian P, Zham H, Mirzaei HR, Shirazi FH. Diagnosis of normal and malignant human gastric tissue samples by FTIR spectra combined with mathematical models. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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44
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Kothari R, Jones V, Mena D, Bermúdez Reyes V, Shon Y, Smith JP, Schmolze D, Cha PD, Lai L, Fong Y, Storrie-Lombardi MC. Raman spectroscopy and artificial intelligence to predict the Bayesian probability of breast cancer. Sci Rep 2021; 11:6482. [PMID: 33753760 PMCID: PMC7985361 DOI: 10.1038/s41598-021-85758-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/03/2021] [Indexed: 01/31/2023] Open
Abstract
This study addresses the core issue facing a surgical team during breast cancer surgery: quantitative prediction of tumor likelihood including estimates of prediction error. We have previously reported that a molecular probe, Laser Raman spectroscopy (LRS), can distinguish healthy and tumor tissue. We now report that combining LRS with two machine learning algorithms, unsupervised k-means and stochastic nonlinear neural networks (NN), provides rapid, quantitative, probabilistic tumor assessment with real-time error analysis. NNs were first trained on Raman spectra using human expert histopathology diagnostics as gold standard (74 spectra, 5 patients). K-means predictions using spectral data when compared to histopathology produced clustering models with 93.2-94.6% accuracy, 89.8-91.8% sensitivity, and 100% specificity. NNs trained on k-means predictions generated probabilities of correctness for the autonomous classification. Finally, the autonomous system characterized an extended dataset (203 spectra, 8 patients). Our results show that an increase in DNA|RNA signal intensity in the fingerprint region (600-1800 cm-1) and global loss of high wavenumber signal (2800-3200 cm-1) are particularly sensitive LRS warning signs of tumor. The stochastic nature of NNs made it possible to rapidly generate multiple models of target tissue classification and calculate the inherent error in the probabilistic estimates for each target.
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Affiliation(s)
- Ragini Kothari
- Department of Surgery, City of Hope National Medical Center, 1500 E. Duarte Rd, Furth 1116, Duarte, CA, 91010, USA.
- Department of Engineering, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA.
| | - Veronica Jones
- Department of Surgery, City of Hope National Medical Center, 1500 E. Duarte Rd, Furth 1116, Duarte, CA, 91010, USA
| | - Dominique Mena
- Department of Engineering, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
| | - Viviana Bermúdez Reyes
- Department of Engineering, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
| | - Youkang Shon
- Department of Engineering, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
| | - Jennifer P Smith
- Department of Physics, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
| | - Daniel Schmolze
- Department of Pathology, City of Hope, 1500 E. Duarte Rd, Duarte, CA, 91010, USA
| | - Philip D Cha
- Department of Engineering, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
| | - Lily Lai
- Department of Surgery, City of Hope National Medical Center, 1500 E. Duarte Rd, Furth 1116, Duarte, CA, 91010, USA
| | - Yuman Fong
- Department of Surgery, City of Hope National Medical Center, 1500 E. Duarte Rd, Furth 1116, Duarte, CA, 91010, USA
| | - Michael C Storrie-Lombardi
- Department of Physics, Harvey Mudd College, 301 Platt Blvd, Claremont, CA, 91711, USA
- Kinohi Institute, Inc, Santa Barbara, CA, 93109, USA
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Gogone ICVP, Ferreira GH, Gava D, Schaefer R, de Paula-Lopes FF, Rocha RDA, de Barros FRO. Applicability of Raman spectroscopy on porcine parvovirus and porcine circovirus type 2 detection. Spectrochim Acta A Mol Biomol Spectrosc 2021; 249:119336. [PMID: 33385972 DOI: 10.1016/j.saa.2020.119336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
Porcine parvovirus (PPV) is one of the major infectious causes of reproductive failure of swine. This disease is characterized by embryonic and fetal infection and death, responsible for important economic losses. PPV is also implicated as a trigger in the development of post-weaning multisystemic wasting syndrome (PMWS) caused by Porcine circovirus type 2 (PCV2). Their detection is PCR-based, which is quite sensitive and specific, but laborious, costly and time-demanding. Therefore, this study aimed to assess Raman spectroscopy (RS) as a diagnostic tool for PPV and PCV2 due to its label-free properties and unique ability to search and identify molecular fingerprints. Briefly, swine testis (ST) cells were inoculated with PPV or PCV2 and in vitro cultured (37 °C, 5% CO2) for four days. Fixed cells were then submitted to RS investigation using a 633 nm laser. A total of 225 spectra centered at 1300 cm-1 was obtained for each sample (5 spectra/cell; 15 cells/replicate; 3 replicates) of PPV-, PCV2-infected and uninfected (control) ST cells. Clear statistical discrimination between samples from both virus-infected cells was achieved with a Principal Component - Linear Discriminant Analysis (PCA-LDA) model, reaching sensitivity rates from 95.55% to 97.77%, respectively to PCV2- and PPV-infected cells. These results were then submitted to a Leave-One-Out (LOO) validation algorithm resulting in 99.97% of accuracy. Extensive band assignment was analyzed and compiled for better understanding of PPV and PCV2 virus-cell interaction, demonstrating that specific protein, lipids and DNA/RNA bands are the most important assignments related to discrimination of virus-infected from uninfected cells. In conclusion, these results represent promising bases for RS application on PCV2 and PPV detection for future diagnostic applications.
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Affiliation(s)
| | | | | | | | | | - Raquel de A Rocha
- Universidade Tecnológica Federal do Paraná, Dois Vizinhos, PR, Brazil
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Miyamori D, Uemura T, Zhu W, Fujikawa K, Nakaya T, Teramukai S, Pezzotti G, Ikegaya H. A Raman algorithm to estimate human age from protein structural variations in autopsy skin samples: a protein biological clock. Sci Rep 2021; 11:5949. [PMID: 33723323 DOI: 10.1038/s41598-021-85371-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/01/2021] [Indexed: 11/29/2022] Open
Abstract
The recent increase of the number of unidentified cadavers has become a serious problem throughout the world. As a simple and objective method for age estimation, we attempted to utilize Raman spectrometry for forensic identification. Raman spectroscopy is an optical-based vibrational spectroscopic technique that provides detailed information regarding a sample’s molecular composition and structures. Building upon our previous proof-of-concept study, we measured the Raman spectra of abdominal skin samples from 132 autopsy cases and the protein-folding intensity ratio, RPF, defined as the ratio between the Raman signals from a random coil an α-helix. There was a strong negative correlation between age and RPF with a Pearson correlation coefficient of r = 0.878. Four models, based on linear (RPF), squared (RPF2), sex, and RPF by sex interaction terms, were examined. The results of cross validation suggested that the second model including linear and squared terms was the best model with the lowest root mean squared error (11.3 years of age) and the highest coefficient of determination (0.743). Our results indicate that the there was a high correlation between the age and RPF and the Raman biological clock of protein folding can be used as a simple and objective forensic age estimation method for unidentified cadavers.
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Mowbray M, Banbury C, Rickard JJS, Davies DJ, Goldberg Oppenheimer P. Development and Characterization of a Probe Device toward Intracranial Spectroscopy of Traumatic Brain Injury. ACS Biomater Sci Eng 2021; 7:1252-1262. [PMID: 33617217 PMCID: PMC7944476 DOI: 10.1021/acsbiomaterials.0c01156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Traumatic
brain injury is a leading cause of mortality worldwide,
often affecting individuals at their most economically active yet
no primary disease-modifying interventions exist for their treatment.
Real-time direct spectroscopic examination of the brain tissue within
the context of traumatic brain injury has the potential to improve
the understanding of injury heterogeneity and subtypes, better target
management strategies and organ penetrance of pharmacological agents,
identify novel targets for intervention, and allow a clearer understanding
of fundamental biochemistry evolution. Here, a novel device is designed
and engineered, delivering Raman spectroscopy-based measurements from
the brain through clinically established cranial access techniques.
Device prototyping is undertaken within the constraints imposed by
the acquisition and site dimensions (standard intracranial access
holes, probe’s dimensions), and an artificial skull anatomical
model with cortical impact is developed. The device shows a good agreement
with the data acquired via a standard commercial
Raman, and the spectra measured are comparable in terms of quality
and detectable bands to the established traumatic brain injury model.
The developed proof-of-concept device demonstrates the feasibility
for real-time optical brain spectroscopic interface while removing
the noise of extracranial tissue and with further optimization and in vivo validation, such technology will be directly translatable
for integration into currently available standards of neurological
care.
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Affiliation(s)
- Max Mowbray
- Department of Chemical Engineering and Analytical Science, University of Manchester, The Mill, Sackwville Street, Manchester M1 3AL, U.K
| | - Carl Banbury
- School of Biochemical Engineering, EPS, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Jonathan J S Rickard
- School of Biochemical Engineering, EPS, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Department of Physics, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K
| | - David J Davies
- Department of Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, National Institute for Health Research, Queen Elizabeth Hospital Birmingham, University of Birmingham, Mindelsohn Way, Birmingham B15 2TH, U.K
| | - Pola Goldberg Oppenheimer
- School of Biochemical Engineering, EPS, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.,Healthcare Technologies Institute, Institute of Translational Medicine, Mindelsohn Way, Birmingham B15 2TH, U.K
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48
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Logan BG, Hopkins DL, Schmidtke LM, Fowler SM. Authenticating common Australian beef production systems using Raman spectroscopy. Food Control 2021; 121:107652. [DOI: 10.1016/j.foodcont.2020.107652] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Holl M, Becker L, Keller AL, Feuerer N, Marzi J, Carvajal Berrio DA, Jakubowski P, Neis F, Pauluschke-Fröhlich J, Brucker SY, Schenke-Layland K, Krämer B, Weiss M. Laparoscopic Peritoneal Wash Cytology-Derived Primary Human Mesothelial Cells for In Vitro Cell Culture and Simulation of Human Peritoneum. Biomedicines 2021; 9:176. [PMID: 33578986 PMCID: PMC7916778 DOI: 10.3390/biomedicines9020176] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/27/2022] Open
Abstract
Peritoneal mucosa of mesothelial cells line the abdominal cavity, surround intestinal organs and the female reproductive organs and are responsible for immunological integrity, organ functionality and regeneration. Peritoneal diseases range from inflammation, adhesions, endometriosis, and cancer. Efficient technologies to isolate and cultivate healthy patient-derived mesothelial cells with maximal purity enable the generation of capable 2D and 3D as well as in vivo-like microfluidic cell culture models to investigate pathomechanisms and treatment strategies. Here, we describe a new and easily reproducible technique for the isolation and culture of primary human mesothelial cells from laparoscopic peritoneal wash cytology. We established a protocol containing multiple washing and centrifugation steps, followed by cell culture at the highest purity and over multiple passages. Isolated peritoneal mesothelial cells were characterized in detail, utilizing brightfield and immunofluorescence microscopy, flow cytometry as well as Raman microspectroscopy and multivariate data analysis. Thereby, cytokeratin expression enabled specific discrimination from primary peritoneal human fibroblasts. Raman microspectroscopy and imaging were used to study morphology and biochemical properties of primary mesothelial cell culture compared to cryo-fixed and cryo-sectioned peritoneal tissue.
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Affiliation(s)
- Myriam Holl
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
| | - Lucas Becker
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies, Eberhard Karls University, 72076 Tübingen, Germany
| | - Anna-Lena Keller
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
| | - Nora Feuerer
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
| | - Julia Marzi
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies, Eberhard Karls University, 72076 Tübingen, Germany
| | - Daniel A. Carvajal Berrio
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies, Eberhard Karls University, 72076 Tübingen, Germany
| | - Peter Jakubowski
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
| | - Felix Neis
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
| | - Jan Pauluschke-Fröhlich
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
| | - Sara Y. Brucker
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
| | - Katja Schenke-Layland
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
- Cluster of Excellence iFIT (EXC 2180) Image-Guided and Functionally Instructed Tumor Therapies, Eberhard Karls University, 72076 Tübingen, Germany
- Department of Medicine/Cardiology, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Bernhard Krämer
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
| | - Martin Weiss
- Department of Women’s Health, Eberhard Karls University, 72076 Tübingen, Germany; (M.H.); (L.B.); (N.F.); (J.M.); (D.A.C.B.); (P.J.); (F.N.); (J.P.-F.); (S.Y.B.); (K.S.-L.); (B.K.)
- NMI Natural and Medical Sciences Institute, University of Tübingen, 72770 Reutlingen, Germany;
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Li H, Ning T, Yu F, Chen Y, Zhang B, Wang S. Raman Microspectroscopic Investigation and Classification of Breast Cancer Pathological Characteristics. Molecules 2021; 26:molecules26040921. [PMID: 33572420 PMCID: PMC7916258 DOI: 10.3390/molecules26040921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Breast cancer is one of the major cancers of women in the world. Despite significant progress in its treatment, an early diagnosis can effectively reduce its incidence rate and mortality. To improve the reliability of Raman-based tumor detection and analysis methods, we conducted an ex vivo study to unveil the compositional features of healthy control (HC), solid papillary carcinoma (SPC), mucinous carcinoma (MC), ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC) tissue samples. Following the identification of biological variations occurring as a result of cancer invasion, principal component analysis followed by linear discriminate analysis (PCA-LDA) algorithm were adopted to distinguish spectral variations among different breast tissue groups. The achieved results confirmed that after training, the constructed classification model combined with the leave-one-out cross-validation (LOOCV) method was able to distinguish the different breast tissue types with 100% overall accuracy. The present study demonstrates that Raman spectroscopy combined with multivariate analysis technology has considerable potential for improving the efficiency and performance of breast cancer diagnosis.
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MESH Headings
- Adenocarcinoma, Mucinous/pathology
- Adenocarcinoma, Mucinous/surgery
- Algorithms
- Breast Neoplasms/classification
- Breast Neoplasms/pathology
- Breast Neoplasms/surgery
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/surgery
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/surgery
- Carcinoma, Papillary/pathology
- Carcinoma, Papillary/surgery
- Case-Control Studies
- Discriminant Analysis
- Female
- Follow-Up Studies
- Humans
- Middle Aged
- Principal Component Analysis
- Spectrum Analysis, Raman/methods
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