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Guler A, Yilmaz A, Oncer N, Sever NI, Cengiz Sahin S, Kavakcıoglu Yardimci B, Yilmaz M. Machine learning-assisted SERS approach enables the biochemical discrimination in Bcl-2 and Mcl-1 expressing yeast cells treated with ketoconazole and fluconazole antifungals. Talanta 2024; 276:126248. [PMID: 38776770 DOI: 10.1016/j.talanta.2024.126248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Antifungal medications are important due to their potential application in cancer treatment either on their own or with traditional treatments. The mechanisms that prevent the effects of these medications and restrict their usage in cancer treatment are not completely understood. The evaluation and discrimination of the possible protective effects of the anti-apoptotic members of the Bcl-2 family of proteins, critical regulators of mitochondrial apoptosis, against antifungal drug-induced cell death has still scientific uncertainties that must be considered. Novel, simple, and reliable strategies are highly demanded to identify the biochemical signature of this phenomenon. However, the complex nature of cells poses challenges for the analysis of cellular biochemical changes or classification. In this study, for the first time, we investigated the probable protective activities of Bcl-2 and Mcl-1 proteins against cell damage induced by ketoconazole (KET) and fluconazole (FLU) antifungal drugs in a yeast model through surface-enhanced Raman spectroscopy (SERS) approach. The proposed SERS platform created robust Raman spectra with a high signal-to-noise ratio. The analysis of SERS spectral data via advanced unsupervised and supervised machine learning methods enabled unquestionable differentiation (100 %) in samples and biomolecular identification. Various SERS bands related to lipids and proteins observed in the analyses suggest that the expression of these anti-apoptotic proteins reduces oxidative biomolecule damage induced by the antifungals. Also, cell viability assay, Annexin V-FITC/PI double staining, and total oxidant and antioxidant status analyses were performed to support Raman measurements. We strongly believe that the proposed approach paves the way for the evaluation of various biochemical structures/changes in various cells.
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Affiliation(s)
- Ayşenur Guler
- Chemistry Department, Graduate School of Natural and Applied Sciences, Pamukkale University, Denizli, Turkey
| | - Asli Yilmaz
- Department of Molecular Biology & Genetics, Faculty of Science, Ataturk University, Erzurum, Turkey
| | - Nazli Oncer
- Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Sciences, Ataturk University, Erzurum, Turkey
| | - Nurettin Ilter Sever
- Department of Molecular Biology & Genetics, Faculty of Science, Pamukkale University, Denizli, Turkey
| | - Sevilay Cengiz Sahin
- Department of Molecular Biology & Genetics, Faculty of Science, Pamukkale University, Denizli, Turkey
| | - Berna Kavakcıoglu Yardimci
- Department of Chemistry, Faculty of Science, Pamukkale University, Denizli, Turkey; Advanced Technology Application and Research Center, Pamukkale University, Denizli, Turkey.
| | - Mehmet Yilmaz
- Department of Nanoscience and Nanoengineering, Graduate School of Natural and Applied Sciences, Ataturk University, Erzurum, Turkey; Department of Chemical Engineering, Faculty of Engineering, Ataturk University, Erzurum, Turkey.
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2
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da Silva TG, Morais CLM, Santos MCD, de Lima LAS, de Medeiros Freitas RV, Guerra RO, Lima KMG. Spectrochemical analysis of blood combined with chemometric techniques for detecting osteosarcopenia. Sci Rep 2023; 13:9686. [PMID: 37322087 PMCID: PMC10272198 DOI: 10.1038/s41598-023-36834-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/10/2023] [Indexed: 06/17/2023] Open
Abstract
Among several complications related to physiotherapy, osteosarcopenia is one of the most frequent in elderly patients. This condition is limiting and quite harmful to the patient's health by disabling several basic musculoskeletal activities. Currently, the test to identify this health condition is complex. In this study, we use mid-infrared spectroscopy combined with chemometric techniques to identify osteosarcopenia based on blood serum samples. The purpose of this study was to evaluate the mid-infrared spectroscopy power to detect osteosarcopenia in community-dwelling older women (n = 62, 30 from patients with osteosarcopenia and 32 healthy controls). Feature reduction and selection techniques were employed in conjunction with discriminant analysis, where a principal component analysis with support vector machines (PCA-SVM) model achieved 89% accuracy to distinguish the samples from patients with osteosarcopenia. This study shows the potential of using infrared spectroscopy of blood samples to identify osteosarcopenia in a simple, fast and objective way.
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Affiliation(s)
- Tales Gomes da Silva
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
| | - Camilo L M Morais
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
| | - Marfran C D Santos
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
- Federal Institute of Education, Science and Technology of Sertão Pernambucano, Floresta, 56400-000, Brazil
| | | | | | - Ricardo Oliveira Guerra
- Postgraduation Program in Health Sciences, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
- Postgraduation Program in Physiotherapy, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
- Department of Physiotherapy, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil
| | - Kássio M G Lima
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59075-970, Brazil.
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3
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Xie L, Wang J, Wang N, Zhu J, Yin Q, Guo R, Duan J, Wang S, Hao C, Shen X. Identification of acute myeloid leukemia by infrared difference spectrum of peripheral blood. J Pharm Biomed Anal 2023; 233:115454. [PMID: 37178631 DOI: 10.1016/j.jpba.2023.115454] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/31/2023] [Accepted: 05/09/2023] [Indexed: 05/15/2023]
Abstract
Acute myeloid leukemia (AML) is a high mortality and recurrence rates hematologic malignancy. Thus, whatever early detection or subsequent visit are both of high significance. Traditional AML diagnosis is conducted via peripheral blood (PB) smear and bone marrow (BM) aspiration. But BM aspiration is a painful burden for patients especially in early detection or subsequent visit. Herein, the use of PB to evaluate and identify the leukemia characteristics will be an attractive alternative source for early detection or subsequent visit. Fourier transform infrared spectroscopy (FTIR) is a time- and cost-effective approach to reveal the disease-related molecular features and variations. However, to the best of our knowledge, there is no attempts using infrared spectroscopic signatures of PB to replace BM for identifying AML. In this work, we are the first to develop a rapid and minimally invasive method to identify AML by infrared difference spectrum (IDS) of PB with only 6 characteristic wavenumbers. We dissect the leukemia-related spectroscopic signatures of three subtypes of leukemia cells (U937, HL-60, THP-1) by IDS, revealing biochemical molecular information about leukemia for the first time. Furthermore, the novel study links cellular features to complex features of blood system which demonstrates the sensitivity and specificity with IDS method. On this basis, BM and PB of AML patients and healthy controls were provided to parallel comparison. The IDS of BM and PB combined with principal component analysis method revealing that the leukemic components in BM and PB can be described by IDS peaks of PCA loadings, respectively. It is demonstrated that the leukemic IDS signatures of BM can be replaced by the leukemic IDS signatures of PB. In addition, the IDS signatures of leukemia cells are reflected in PB of AML patients with peaks of 1629, 1610, 1604, 1536, 1528 and 1404 cm-1 for the first time as well. To this end, we access the leukemic signatures of IDS peaks to compare the PB of AMLs and healthy controls. It is confirmed that the leukemic components can be detected from PB of AML and distinguished into positive (100%) and negative (100%) groups successfully by IDS classifier which is a novel and unique spectral classifier. This work demonstrates the potential use of IDS as a powerful tool to detect leukemia via PB which can release subjects' pain remarkably.
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Affiliation(s)
- Leiying Xie
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China; School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- The Hematological Dept. Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Na Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianguo Zhu
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Qianqian Yin
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, §School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruobing Guo
- Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Kongjiang Road 1665, Shanghai 200092, China
| | - Junli Duan
- Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Kongjiang Road 1665, Shanghai 200092, China
| | - Shaowei Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Changning Hao
- Xinhua Hospital affiliated to Shanghai Jiaotong University School of Medicine, Kongjiang Road 1665, Shanghai 200092, China.
| | - Xuechu Shen
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China; School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Alves MVS, Maciel LIL, Passos JOS, Morais CLM, Dos Santos MCD, Lima LAS, Vaz BG, Pegado R, Lima KMG. Spectrochemical approach combined with symptoms data to diagnose fibromyalgia through paper spray ionization mass spectrometry (PSI-MS) and multivariate classification. Sci Rep 2023; 13:4658. [PMID: 36949149 PMCID: PMC10033633 DOI: 10.1038/s41598-023-31565-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/14/2023] [Indexed: 03/24/2023] Open
Abstract
This study performs a chemical investigation of blood plasma samples from patients with and without fibromyalgia, combined with some of the symptoms and their levels of intensity used in the diagnosis of this disease. The symptoms evaluated were: visual analogue pain scale (VAS); fibromyalgia impact questionnaire (FIQ); Hamilton anxiety rating scale (HAM); Tampa Scale for Kinesiophobia (TAMPA); quality of life Questionnaire-physical and mental health (QL); and Pain Catastrophizing Scale (CAT). Plasma samples were analyzed by paper spray ionization mass spectrometry (PSI-MS). Spectral data were organized into datasets and related to each of the symptoms measured. The datasets were submitted to multivariate classification using supervised models such as principal component analysis with linear discriminant analysis (PCA-LDA), successive projections algorithm with linear discriminant analysis (SPA-LDA), genetic algorithm with linear discriminant analysis (GA-LDA) and their versions with quadratic discriminant analysis (PCA/SPA/GA-QDA) and support vector machines (PCA/SPA/GA-SVM). These algorithm combinations were performed aiming the best class separation. Good discrimination between the controls and fibromyalgia samples were observed using PCA-LDA, where the spectral data associated with the CAT symptom achieved 100% classification sensitivity, and associated with the VAS symptom achieved 100% classification specificity, with both symptoms at the moderate level of intensity. The spectral variable at 579 m/z was found to be substantially significant for classification according to the PCA loadings. According to the human metabolites database, this variable can be associated with a LysoPC compound, which comprises a class of metabolites already evidenced in other studies for fibromyalgia diagnosis. This study proposed an investigation of spectral data combined with clinical data to compare the classification ability of different datasets. The good classification results obtained confirm this technique is as a good analytical tool for the detection of fibromyalgia, and provides theoretical support for other studies about fibromyalgia diagnosis.
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Affiliation(s)
- Marcelo V S Alves
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Lanaia I L Maciel
- Institute of Chemistry, Federal University of Goiás, Samambaia St., Goiânia, GO, 74690-900, Brazil
| | - João O S Passos
- Health Sciences Center, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Camilo L M Morais
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Marfran C D Dos Santos
- Federal Institute of Education, Science and Technology of Sertão Pernambucano, Floresta, Brazil
| | - Leomir A S Lima
- Estácio de Sá Goiás, North Regional, Goiânia, GO, 74063-010, Brazil
| | - Boniek G Vaz
- Institute of Chemistry, Federal University of Goiás, Samambaia St., Goiânia, GO, 74690-900, Brazil
| | - Rodrigo Pegado
- Health Sciences Center, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Kássio M G Lima
- Institute of Chemistry, Biological Chemistry and Chemometrics, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil.
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5
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Schiemer R, Furniss D, Phang S, Seddon AB, Atiomo W, Gajjar KB. Vibrational Biospectroscopy: An Alternative Approach to Endometrial Cancer Diagnosis and Screening. Int J Mol Sci 2022; 23:ijms23094859. [PMID: 35563249 PMCID: PMC9102412 DOI: 10.3390/ijms23094859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer and the fourth leading cause of death among women worldwide. Early detection and treatment are associated with a favourable prognosis and reduction in mortality. Unlike other common cancers, however, screening strategies lack the required sensitivity, specificity and accuracy to be successfully implemented in clinical practice and current diagnostic approaches are invasive, costly and time consuming. Such limitations highlight the unmet need to develop diagnostic and screening alternatives for EC, which should be accurate, rapid, minimally invasive and cost-effective. Vibrational spectroscopic techniques, Mid-Infrared Absorption Spectroscopy and Raman, exploit the atomic vibrational absorption induced by interaction of light and a biological sample, to generate a unique spectral response: a “biochemical fingerprint”. These are non-destructive techniques and, combined with multivariate statistical analysis, have been shown over the last decade to provide discrimination between cancerous and healthy samples, demonstrating a promising role in both cancer screening and diagnosis. The aim of this review is to collate available evidence, in order to provide insight into the present status of the application of vibrational biospectroscopy in endometrial cancer diagnosis and screening, and to assess future prospects.
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Affiliation(s)
- Roberta Schiemer
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
- Correspondence:
| | - David Furniss
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Sendy Phang
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Angela B. Seddon
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - William Atiomo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai P.O. Box 505055, United Arab Emirates;
| | - Ketankumar B. Gajjar
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
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6
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Jales JT, Barbosa TM, de Medeiros JR, de Lima LAS, de Lima KMG, Gama RA. Infrared spectroscopy and forensic entomology: Can this union work? A literature review. J Forensic Sci 2021; 66:2080-2091. [PMID: 34291458 DOI: 10.1111/1556-4029.14800] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/11/2021] [Accepted: 06/01/2021] [Indexed: 12/01/2022]
Abstract
For more than two decades, infrared spectroscopy techniques combined with multivariate analysis have been efficiently applied in several entomological fields, such as Taxonomy and Toxicology. However, little is known about its use and applicability in Forensic entomology (FE) field, with vibrational techniques such as Near-infrared spectroscopy (NIRS) and Medium-infrared spectroscopy (MIRS) underutilized in forensic sciences. Thus, this work describes the potential of NIRS, MIRS, and other spectroscopic methodologies, for entomological analysis in FE, as well as discusses its future uses for criminal or civil investigations. After a thorough research on scientific journals database, a total of 33 publications were found in scientific journals, with direct or indirect application to FE, including experimental applications of NIRS and MIRS in taxonomic discrimination of species, larval age prediction, detection of toxic substances in insects from environments or crime scenes, and detection of internal or external infestations by live or dead insects in stored products. Besides, NIRS and MIRS combined with multivariate analysis were efficient, inexpensive, fast, and non-destructive analytical tools. However, more than 51% of the spectroscopic publications are concentrated in the stored products field, and so we discuss the need for expansion and more direct application in other FE areas. We hope the number of articles continues to increase, and as NIRS and MIRS technology progress, they advance in forensic research and routine use.
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Affiliation(s)
- Jessica T Jales
- Laboratory of Insect and Vectors, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Biochemistry and Molecular Biology post-graduation program, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Taciano M Barbosa
- Laboratory of Insect and Vectors, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Parasitic biology post-graduation program, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Jucélia R de Medeiros
- Laboratory of Insect and Vectors, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Parasitic biology post-graduation program, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Leomir A S de Lima
- Laboratory of Biological Chemistry and Chemometric, Department of Chemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Kássio M G de Lima
- Laboratory of Biological Chemistry and Chemometric, Department of Chemistry, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Renata A Gama
- Laboratory of Insect and Vectors, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil.,Parasitic biology post-graduation program, Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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7
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Dizaji AN, Ozek NS, Yilmaz A, Aysin F, Yilmaz M. Gold nanorod arrays enable highly sensitive bacterial detection via surface-enhanced infrared absorption (SEIRA) spectroscopy. Colloids Surf B Biointerfaces 2021; 206:111939. [PMID: 34186307 DOI: 10.1016/j.colsurfb.2021.111939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 12/26/2022]
Abstract
Infrared (IR) spectroscopy is a unique and powerful method in the identification, characterization, and classification of chemical and biological molecules. However, the low absorbance of biological molecules has arisen as a major bottleneck and inhibits the application of IR in practical applications. To overcome this limitation, in the last four decades, surface-enhanced IR absorption (SEIRA) spectroscopy has been proposed and has become the focus of interest in various applications. In this study, for the first time, we proposed the employment of 3D anisotropic gold nanorod arrays (GNAs) as a highly active SEIRA platform in bacterial detection. For this, GNA platforms were fabricated through an oblique angle deposition (OAD) approach by using a physical vapor deposition (PVD) system. OAD of gold at proper deposition angle (10°) created closely-packed and columnar gold nanorod structures onto the glass slides in a well-controlled manner. GNA platform was tested as a SEIRA system in three different species of bacteria (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis) by collecting IR spectra of each bacteria from different parts of GNA. The employment of GNA provided robust IR spectra with high reproducibility and signal-to-noise ratio. For the comparison, IR spectra of each bacteria were collected from aluminum foil and a smooth gold surface (SGS). No or very low IR spectra were observed in comparison to the GNA platform for these substrates. Unsupervised (PCA, HCA) and supervised (SIMCA, LDA, and SVM classification) machine learning analysis of bacteria spectra obtained from GNA substrate indicated that all bacteria samples can be detected and identified without using a label-containing biosensor, in a fast and simple manner.
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Affiliation(s)
- Araz Norouz Dizaji
- Department of Chemical Engineering, Ataturk University, 25240 Erzurum, Turkey; East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey
| | - Nihal Simsek Ozek
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Biology, Ataturk University, 25240 Erzurum, Turkey
| | - Asli Yilmaz
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Molecular Biology and Genetics, Ataturk University, 25240 Erzurum, Turkey
| | - Ferhunde Aysin
- East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Biology, Ataturk University, 25240 Erzurum, Turkey
| | - Mehmet Yilmaz
- Department of Chemical Engineering, Ataturk University, 25240 Erzurum, Turkey; East Anatolia High Technology Application and Research Center (DAYTAM), Ataturk University, 25240 Erzurum, Turkey; Department of Nanoscience and Nanoengineering, Ataturk University, 25240 Erzurum, Turkey.
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8
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Neves ACO, Viana AD, Menezes FG, Wanderlei Neto AO, Melo MCN, Gasparotto LHS. Biospectroscopy and chemometrics as an analytical tool for comparing the antibacterial mechanism of silver nanoparticles with popular antibiotics against Escherichia coli. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 253:119558. [PMID: 33631629 DOI: 10.1016/j.saa.2021.119558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/22/2021] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Despite the fact that silver nanoparticles (AgNPs) have been widely studied in medical and correlated fields, details on their mechanisms are yet to be fully understood. Herein we present the first study on the combination of infrared spectroscopy and chemometrics as an analytical tool to investigate the mechanism of action of AgNPs against Escherichia coli by comparison with popular and commercially available antibiotics. The rationale behind this study is that the selected antibiotics act on bacteria in specific and distinct manners (DNA, cell membrane, mitochondria, etc.). Hence, via multivariate analysis we were able to compare the spectra of bacteria treated with the antibiotics and AgNPs to determine the main target of the latter. Spectral comparison, exploratory analysis, clustering and classification based on infrared spectra were carried out for E. coli samples in the absence and presence (treated) of four widely known antibiotics (ampicillin, ciprofloxacin, gentamicin and sulfadiazine) as well as RA-AgNPs and ERA-AgNPs. Chemometrics models indicated an interesting similarity between infrared spectra from E. coli treated with sulfadiazine and AgNPs, in which vibrational modes associated to phosphate groups were found to be the most representative. This result suggests that both AgNPs and sulfadiazine affects DNA structural features and availability, but not necessarily through the same mechanism. This biospectroscopy-based approach opens an interesting possibility for the understanding over the mechanism of antibacterial activity of AgNPs.
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Affiliation(s)
- Ana C O Neves
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil.
| | - Anderson D Viana
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil; Agricultural School of Jundiaí, Federal University of Rio Grande do Norte, Macaíba, RN 59280-000, Brazil
| | - Fabrício G Menezes
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil
| | | | - Maria Celeste N Melo
- Department of Microbiology and Parasitology, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil
| | - Luiz H S Gasparotto
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN 59072-970, Brazil
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9
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Ribeiro da Cunha B, Fonseca LP, Calado CRC. Simultaneous elucidation of antibiotic mechanism of action and potency with high-throughput Fourier-transform infrared (FTIR) spectroscopy and machine learning. Appl Microbiol Biotechnol 2021; 105:1269-1286. [PMID: 33443637 DOI: 10.1007/s00253-021-11102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/09/2020] [Accepted: 01/05/2021] [Indexed: 12/15/2022]
Abstract
The low rate of discovery and rapid spread of resistant pathogens have made antibiotic discovery a worldwide priority. In cell-based screening, the mechanism of action (MOA) is identified after antimicrobial activity. This increases rediscovery, impairs low potency candidate detection, and does not guide lead optimization. In this study, high-throughput Fourier-transform infrared (FTIR) spectroscopy was used to discriminate the MOA of 14 antibiotics at pathway, class, and individual antibiotic level. For that, the optimal combinations and parametrizations of spectral preprocessing were selected with cross-validated partial least squares discriminant analysis, to which various machine learning algorithms were applied. This coherently resulted in very good accuracies, independently of the algorithms, and at all levels of MOA. Particularly, an ensemble of subspace discriminants predicted the known pathway (98.6%), antibiotic classes (100%), and individual antibiotics (97.8%) with exceptional accuracy, and similar results were obtained for simulated novel MOA. Even at very low concentrations (1 μg/mL) and growth inhibition (15%), over 70% pathway and class accuracy was achieved, suggesting FTIR spectroscopy can probe the grey chemical matter. Prediction of inhibitory effect was also examined, for which a squared exponential Gaussian process regression yielded a root mean square error of 0.33 and a R2 of 0.92, indicating that metabolic alterations leading to growth inhibition are intrinsically reflected on FTIR spectra beyond cell density. KEY POINTS: • Antibiotic MOA and potency estimated with high-throughput FTIR spectroscopy • Sub-inhibitory MOA identification suggests ability to explore grey chemical matter • Data analysis optimization improved MOA identification at antibiotic level by 38.
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Affiliation(s)
- Bernardo Ribeiro da Cunha
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal. .,Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
| | - Luís P Fonseca
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa (UL), Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Departamento de Engenharia Química, ISEL - Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa (IPL), R. Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal
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10
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Bernardes-Oliveira E, de Freitas DLD, de Morais CDLM, Cornetta MDCDM, Camargo JDDAS, de Lima KMG, Crispim JCDO. Spectrochemical differentiation in gestational diabetes mellitus based on attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy and multivariate analysis. Sci Rep 2020; 10:19259. [PMID: 33159100 PMCID: PMC7648639 DOI: 10.1038/s41598-020-75539-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/30/2020] [Indexed: 11/09/2022] Open
Abstract
Gestational diabetes mellitus (GDM) is a hyperglycaemic imbalance first recognized during pregnancy, and affects up to 22% of pregnancies worldwide, bringing negative maternal–fetal consequences in the short- and long-term. In order to better characterize GDM in pregnant women, 100 blood plasma samples (50 GDM and 50 healthy pregnant control group) were submitted Attenuated Total Reflection Fourier-transform infrared (ATR-FTIR) spectroscopy, using chemometric approaches, including feature selection algorithms associated with discriminant analysis, such as Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA) and Support Vector Machines (SVM), analyzed in the biofingerprint region between 1800 and 900 cm−1 followed by Savitzky–Golay smoothing, baseline correction and normalization to Amide-I band (~ 1650 cm−1). An initial exploratory analysis of the data by Principal Component Analysis (PCA) showed a separation tendency between the two groups, which were then classified by supervised algorithms. Overall, the results obtained by Genetic Algorithm Linear Discriminant Analysis (GA-LDA) were the most satisfactory, with an accuracy, sensitivity and specificity of 100%. The spectral features responsible for group differentiation were attributed mainly to the lipid/protein regions (1462–1747 cm−1). These findings demonstrate, for the first time, the potential of ATR-FTIR spectroscopy combined with multivariate analysis as a screening tool for fast and low-cost GDM detection.
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Affiliation(s)
- Emanuelly Bernardes-Oliveira
- Post-Graduate Program in Technological Development and Innovation in Medicines, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil.
| | - Daniel Lucas Dantas de Freitas
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Camilo de Lelis Medeiros de Morais
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Fulwood, Preston, PR2 9HT, UK.,School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | | | | | - Kassio Michell Gomes de Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil
| | - Janaina Cristiana de Oliveira Crispim
- Post-Graduate Program in Technological Development and Innovation in Medicines, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil. .,Januario Cicco Maternity School, Federal University of Rio Grande do Norte, Natal, RN, 59072-970, Brazil.
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11
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Spectrochemical analysis in blood plasma combined with subsequent chemometrics for fibromyalgia detection. Sci Rep 2020; 10:11769. [PMID: 32678231 PMCID: PMC7366631 DOI: 10.1038/s41598-020-68781-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
Fibromyalgia is a rheumatologic condition characterized by multiple and chronic body pain, and other typical symptoms such as intense fatigue, anxiety and depression. It is a very complex disease where treatment is often made by non-medicated alternatives in order to alleviate symptoms and improve the patient’s quality of life. Herein, we propose a method to detect patients with fibromyalgia (n = 252, 126 controls and 126 patients with fibromyalgia) through the analysis of their blood plasma using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy in conjunction with chemometric techniques, hence, providing a low-cost, fast and accurate diagnostic approach. Different chemometric algorithms were tested to classify the spectral data; genetic algorithm with linear discriminant analysis (GA-LDA) achieved the best diagnostic results with a sensitivity of 89.5% in an external test set. The GA-LDA model identified 24 spectral wavenumbers responsible for class separation; amongst these, the Amide II (1,545 cm−1) and proteins (1,425 cm−1) were identified to be discriminant features. These results reinforce the potential of ATR-FTIR spectroscopy with multivariate analysis as a new tool to screen and detect patients with fibromyalgia in a fast, low-cost, non-destructive and minimally invasive fashion.
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12
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Tutorial: multivariate classification for vibrational spectroscopy in biological samples. Nat Protoc 2020; 15:2143-2162. [PMID: 32555465 DOI: 10.1038/s41596-020-0322-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/20/2020] [Indexed: 12/26/2022]
Abstract
Vibrational spectroscopy techniques, such as Fourier-transform infrared (FTIR) and Raman spectroscopy, have been successful methods for studying the interaction of light with biological materials and facilitating novel cell biology analysis. Spectrochemical analysis is very attractive in disease screening and diagnosis, microbiological studies and forensic and environmental investigations because of its low cost, minimal sample preparation, non-destructive nature and substantially accurate results. However, there is now an urgent need for multivariate classification protocols allowing one to analyze biologically derived spectrochemical data to obtain accurate and reliable results. Multivariate classification comprises discriminant analysis and class-modeling techniques where multiple spectral variables are analyzed in conjunction to distinguish and assign unknown samples to pre-defined groups. The requirement for such protocols is demonstrated by the fact that applications of deep-learning algorithms of complex datasets are being increasingly recognized as critical for extracting important information and visualizing it in a readily interpretable form. Hereby, we have provided a tutorial for multivariate classification analysis of vibrational spectroscopy data (FTIR, Raman and near-IR) highlighting a series of critical steps, such as preprocessing, data selection, feature extraction, classification and model validation. This is an essential aspect toward the construction of a practical spectrochemical analysis model for biological analysis in real-world applications, where fast, accurate and reliable classification models are fundamental.
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13
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Abstract
Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.
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Affiliation(s)
- Duncan Finlayson
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Christopher Rinaldi
- Centre for Doctoral Training in Medical Devices and Health Technologies, Department of Biomedical Engineering , University of Strathclyde , Wolfson Centre, 106 Rottenrow , Glasgow G4 0NW , U.K.,WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K
| | - Matthew J Baker
- WestCHEM , Department of Pure and Applied Chemistry , Technology and Innovation Centre, 99 George Street , Glasgow G1 1RD , U.K.,ClinSpec Diagnostics Ltd. , Technology and Innovation Centre, 99 George Street , Glasgow G11RD , U.K
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14
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Mansoldo FRP, Neves Junior A, Cardoso VDS, Rosa MDSS, Vermelho AB. Evaluation of Kluyveromyces marxianus endo-polygalacturonase activity through ATR-FTIR. Analyst 2019; 144:4111-4120. [PMID: 31172988 DOI: 10.1039/c9an00265k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The endo-polygalacturonase enzyme (endoPG: EC 3.2.1.15) plays an important role in the fruit juice and wine industries, so the development of new tools for the quantitative and qualitative analysis of its enzymatic action is necessary. In this work, we report the development of a simple, fast and practical method that did not use any chemical reagent to identify and evaluate the action of the endoPG enzyme, produced by the yeast Kluyveromyces marxianus CCT3172, using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy combined with principal component analysis-linear discriminant analysis (PCA-LDA). This method evaluated the action of the endoPG enzyme on the polygalacturonic acid (PGA) substrate at 5 different times (0, 10, 15, 20 and 30 minutes), and at each time interval the samples were analyzed by ATR-FTIR. It was demonstrated that there was clear segregation between the samples that were and that were not subjected to the action of the endoPG enzyme, and it was also possible to distinguish the samples that were subjected to different incubation times with the enzyme. Through PCA-LDA it was possible to obtain wavelengths that are biomarkers for this enzymatic reaction and the observed changes as a function of hydrolysis duration were found to be in agreement with the breakdown of the glycosidic chain (1011 cm-1-CH-O- CH stretching) of PGA and release of oligosaccharides (1078 cm-1 C-OH elongation). The activity of the endoPG enzyme and the release of galacturonic acid were verified by the dinitrosalicylic acid (DNS) method in all samples. The efficacy of an automatic classifier using a principal component analysis-linear discriminant classifier (PCA-LDC) was evaluated to diagnose the action of the endoPG enzyme. The results showed an accuracy of 100% for the identification of the endoPG enzyme action and from 91.67% to 100% for classification according to the hydrolysis duration in which PGA was exposed to endoPG. The present study indicates that this methodology may be a new approach for the qualitative evaluation of the endoPG enzyme with the potential to be used in laboratories and industries.
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Affiliation(s)
- Felipe Raposo Passos Mansoldo
- BIOINOVAR - Biocatalysis, Bioproducts and Bioenergy, Paulo de Góes Institute of Microbiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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15
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Ghosh A, Raha S, Dey S, Chatterjee K, Roy Chowdhury A, Barui A. Chemometric analysis of integrated FTIR and Raman spectra obtained by non-invasive exfoliative cytology for the screening of oral cancer. Analyst 2019; 144:1309-1325. [DOI: 10.1039/c8an02092b] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
FTIR spectroscopy and Raman spectroscopy of biological analytes are increasingly explored as screening tools for early detection of cancer.
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Affiliation(s)
- Aritri Ghosh
- Centre for Healthcare Science and Technology
- Indian Institute of Engineering Science and Technology
- Howrah 711103
- India
| | - Sreyan Raha
- Department of Physics
- Bose Institute
- Kolkata-700009
- India
| | - Susmita Dey
- Centre for Healthcare Science and Technology
- Indian Institute of Engineering Science and Technology
- Howrah 711103
- India
| | - Kabita Chatterjee
- Department of Oral and Maxillofacial Pathology
- Buddha Institute of Dental Sciences
- Patna 800020
- India
| | - Amit Roy Chowdhury
- Department of Aerospace and Applied Mechanics
- Indian Institute of Engineering Science and Technology
- Howrah 711103
- India
| | - Ananya Barui
- Centre for Healthcare Science and Technology
- Indian Institute of Engineering Science and Technology
- Howrah 711103
- India
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16
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Morais CM, Shore RF, Pereira MG, Martin FL. Assessing Binary Mixture Effects from Genotoxic and Endocrine Disrupting Environmental Contaminants Using Infrared Spectroscopy. ACS OMEGA 2018; 3:13399-13412. [PMID: 30411037 PMCID: PMC6217637 DOI: 10.1021/acsomega.8b01916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/04/2018] [Indexed: 05/15/2023]
Abstract
Benzo[a]pyrene (B[a]P), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs) are persistent contaminants and concern has arisen over co-exposure of organisms when the chemicals exist in mixtures. Herein, attenuated total reflection Fourier transform infrared spectroscopy was used to identify biochemical alterations induced in cells by single and binary mixtures of these environmental chemicals. It was also investigated as a method to identify if interactions are occurring in mixtures and as a possible tool to predict mixture effects. Mallard fibroblasts were treated with single and binary mixtures of B[a]P, PCB126, PCB153, BDE47, and BDE209. Comparison of observed spectra from cells treated with binary mixtures with expected additive spectra, which were created from individual exposure spectra, indicated that in many areas of the spectrum, less-than-additive binary mixture effects may occur. However, possible greater-than-additive alterations were identified in the 1650-1750 cm-1 lipid region and may demonstrate a common mechanism of B[a]P and PCBs or PBDEs, which can enhance toxicity in mixtures.
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Affiliation(s)
- Camilo
L. M. Morais
- School
of Pharmacy and Biomedical Sciences, University
of Central Lancashire (UCLan), Preston PR1 2HE, U.K.
| | - Richard F. Shore
- Centre
of Ecology & Hydrology, Lancaster Environment
Centre, Lancaster LA1 4AP, U.K.
| | - M. Glória Pereira
- Centre
of Ecology & Hydrology, Lancaster Environment
Centre, Lancaster LA1 4AP, U.K.
| | - Francis L. Martin
- School
of Pharmacy and Biomedical Sciences, University
of Central Lancashire (UCLan), Preston PR1 2HE, U.K.
- E-mail:
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17
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Pérez MRV, Contreras HRN, Sosa Herrera JA, Ávila JPL, Tobías HMR, Martínez FDB, Ramírez RF, Vázquez ÁGR. Detection of Clavibacter michiganensis subsp. michiganensis Assisted by Micro-Raman Spectroscopy under Laboratory Conditions. THE PLANT PATHOLOGY JOURNAL 2018; 34:381-392. [PMID: 30369848 PMCID: PMC6200046 DOI: 10.5423/ppj.oa.02.2018.0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/10/2018] [Accepted: 05/31/2018] [Indexed: 06/08/2023]
Abstract
Clavibacter michiganensis subsp. michiganesis (Cmm) is a quarantine-worthy pest in México. The implementation and validation of new technologies is necessary to reduce the time for bacterial detection in laboratory conditions and Raman spectroscopy is an ambitious technology that has all of the features needed to characterize and identify bacteria. Under controlled conditions a contagion process was induced with Cmm, the disease epidemiology was monitored. Micro-Raman spectroscopy (532 nm λ laser) technique was evaluated its performance at assisting on Cmm detection through its characteristic Raman spectrum fingerprint. Our experiment was conducted with tomato plants in a completely randomized block experimental design (13 plants × 4 rows). The Cmm infection was confirmed by 16S rDNA and plants showed symptoms from 48 to 72 h after inoculation, the evolution of the incidence and severity on plant population varied over time and it kept an aggregated spatial pattern. The contagion process reached 79% just 24 days after the epidemic was induced. Micro-Raman spectroscopy proved its speed, efficiency and usefulness as a non-destructive method for the preliminary detection of Cmm. Carotenoid specific bands with wavelengths at 1146 and 1510 cm-1 were the distinguishable markers. Chemometric analyses showed the best performance by the implementation of PCA-LDA supervised classification algorithms applied over Raman spectrum data with 100% of performance in metrics of classifiers (sensitivity, specificity, accuracy, negative and positive predictive value) that allowed us to differentiate Cmm from other endophytic bacteria (Bacillus and Pantoea). The unsupervised KMeans algorithm showed good performance (100, 96, 98, 91 y 100%, respectively).
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Affiliation(s)
- Moisés Roberto Vallejo Pérez
- CONACyT-Universidad Autónoma de San Luis Potosí. Álvaro Obregón #64, Col. Centro, C.P. 78000, San Luis Potosí, S.L.P.
México
| | - Hugo Ricardo Navarro Contreras
- Universidad Autónoma de San Luis Potosí. Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología (CIACyT). Av. Sierra Leona #550, Col. Lomas 2a. Sección, C.P. 78210, S.L.P.,
México
| | - Jesús A. Sosa Herrera
- CONACyT-Centro de Investigación en Ciencias de Información Geoespacial A.C. Circuito Tecnopolo Norte 117, Col. Fraccionamiento Tecnopolo Pocitos, CP. 20313, Aguascalientes, Ags.
México
| | - José Pablo Lara Ávila
- Universidad Autónoma de San Luis Potosí. Facultad de Agronomía y Veterinaria. Km. 14.5 Carretera San Luis Potosí, Matehuala, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, C.P. 78321. S.L.P.
México
| | - Hugo Magdaleno Ramírez Tobías
- Universidad Autónoma de San Luis Potosí. Facultad de Agronomía y Veterinaria. Km. 14.5 Carretera San Luis Potosí, Matehuala, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, C.P. 78321. S.L.P.
México
| | - Fernando Díaz-Barriga Martínez
- Universidad Autónoma de San Luis Potosí. Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología (CIACyT). Av. Sierra Leona #550, Col. Lomas 2a. Sección, C.P. 78210, S.L.P.,
México
| | - Rogelio Flores Ramírez
- CONACyT-Universidad Autónoma de San Luis Potosí. Álvaro Obregón #64, Col. Centro, C.P. 78000, San Luis Potosí, S.L.P.
México
| | - Ángel Gabriel Rodríguez Vázquez
- Universidad Autónoma de San Luis Potosí. Coordinación para la Innovación y la Aplicación de la Ciencia y la Tecnología (CIACyT). Av. Sierra Leona #550, Col. Lomas 2a. Sección, C.P. 78210, S.L.P.,
México
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18
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Theophilou G, Morais CLM, Halliwell DE, Lima KMG, Drury J, Martin-Hirsch PL, Stringfellow HF, Hapangama DK, Martin FL. Synchrotron- and focal plane array-based Fourier-transform infrared spectroscopy differentiates the basalis and functionalis epithelial endometrial regions and identifies putative stem cell regions of human endometrial glands. Anal Bioanal Chem 2018; 410:4541-4554. [PMID: 29740671 PMCID: PMC6021468 DOI: 10.1007/s00216-018-1111-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/18/2018] [Accepted: 04/25/2018] [Indexed: 12/19/2022]
Abstract
The cyclical process of regeneration of the endometrium suggests that it may contain a cell population that can provide daughter cells with high proliferative potential. These cell lineages are clinically significant as they may represent clonogenic cells that may also be involved in tumourigenesis as well as endometriotic lesion development. To determine whether the putative stem cell location within human uterine tissue can be derived using vibrational spectroscopy techniques, normal endometrial tissue was interrogated by two spectroscopic techniques. Paraffin-embedded uterine tissues containing endometrial glands were sectioned to 10-μm-thick parallel tissue sections and were floated onto BaF2 slides for synchrotron radiation-based Fourier-transform infrared (SR-FTIR) microspectroscopy and globar focal plane array-based FTIR spectroscopy. Different spectral characteristics were identified depending on the location of the glands examined. The resulting infrared spectra were subjected to multivariate analysis to determine associated biophysical differences along the length of longitudinal and crosscut gland sections. Comparison of the epithelial cellular layer of transverse gland sections revealed alterations indicating the presence of putative transient-amplifying-like cells in the basalis and mitotic cells in the functionalis. SR-FTIR microspectroscopy of the base of the endometrial glands identified the location where putative stem cells may reside at the same time pointing towards νsPO2− in DNA and RNA, nucleic acids and amide I and II vibrations as major discriminating factors. This study supports the view that vibration spectroscopy technologies are a powerful adjunct to our understanding of the stem cell biology of endometrial tissue. ᅟ ![]()
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Affiliation(s)
- Georgios Theophilou
- Department of Gynaecology, Leeds Teaching Hospitals NHS Foundation Trust, Leeds, LS1 3EX, UK
| | - Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Diane E Halliwell
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande do Norte, Natal, 59072-970, Brazil
| | - Josephine Drury
- Department of Obstetrics and Gynaecology, Liverpool Women's NHS Foundation Trust, Liverpool, L8 7SS, UK
| | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Fulwood, Preston, PR2 9HT, UK
| | - Helen F Stringfellow
- Department of Obstetrics and Gynaecology, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Foundation Trust, Fulwood, Preston, PR2 9HT, UK
| | - Dharani K Hapangama
- Department of Obstetrics and Gynaecology, Liverpool Women's NHS Foundation Trust, Liverpool, L8 7SS, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK.
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19
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PG-Metrics: A chemometric-based approach for classifying bacterial peptidoglycan data sets and uncovering their subjacent chemical variability. PLoS One 2017; 12:e0186197. [PMID: 29040278 PMCID: PMC5645090 DOI: 10.1371/journal.pone.0186197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/27/2017] [Indexed: 02/07/2023] Open
Abstract
Bacteria cells are protected from osmotic and environmental stresses by an exoskeleton-like polymeric structure called peptidoglycan (PG) or murein sacculus. This structure is fundamental for bacteria’s viability and thus, the mechanisms underlying cell wall assembly and how it is modulated serve as targets for many of our most successful antibiotics. Therefore, it is now more important than ever to understand the genetics and structural chemistry of the bacterial cell walls in order to find new and effective methods of blocking it for the treatment of disease. In the last decades, liquid chromatography and mass spectrometry have been demonstrated to provide the required resolution and sensitivity to characterize the fine chemical structure of PG. However, the large volume of data sets that can be produced by these instruments today are difficult to handle without a proper data analysis workflow. Here, we present PG-metrics, a chemometric based pipeline that allows fast and easy classification of bacteria according to their muropeptide chromatographic profiles and identification of the subjacent PG chemical variability between e.g. bacterial species, growth conditions and, mutant libraries. The pipeline is successfully validated here using PG samples from different bacterial species and mutants in cell wall proteins. The obtained results clearly demonstrated that PG-metrics pipeline is a valuable bioanalytical tool that can lead us to cell wall classification and biomarker discovery.
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Abstract
This review presents a retrospective of the studies carried out in the last 10 years (2006–2016) using spectroscopic methods as a research tool in the field of virology. Spectroscopic analyses are sensitive to variations in the biochemical composition of the sample, are non-destructive, fast and require the least sample preparation, making spectroscopic techniques tools of great interest in biological studies. Herein important chemometric algorithms that have been used in virological studies are also evidenced as a good alternative for analyzing the spectra, discrimination and classification of samples. Techniques that have not yet been used in the field of virology are also suggested. This methodology emerges as a new and promising field of research, and may be used in the near future as diagnosis tools for detecting diseases caused by viruses. A retrospective study of 2006–2016 using spectroscopic methods as a research tool in the field of virology. Chemometric algorithms used in virological studies were evidenced. This review emerges as a new and promising field of research in virology.
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