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Meng H, Elliott A, Mansfield J, Bailey M, Frogley M, Cinque G, Moger J, Stone N, Tamagnini F, Palombo F. Identification of tauopathy-associated lipid signatures in Alzheimer's disease mouse brain using label-free chemical imaging. Commun Biol 2024; 7:1341. [PMID: 39420210 PMCID: PMC11487145 DOI: 10.1038/s42003-024-07034-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 10/08/2024] [Indexed: 10/19/2024] Open
Abstract
There is cumulative evidence that lipid metabolism plays a key role in the pathogenesis of various neurodegenerative disorders including Alzheimer's disease (AD). Visualising lipid content in a non-destructive label-free manner can aid in elucidating the AD phenotypes towards a better understanding of the disease. In this study, we combined multiple optical molecular-specific methods, Fourier transform infrared (FTIR) spectroscopic imaging, synchrotron radiation-infrared (SR-IR) microscopy, Raman and stimulated Raman scattering (SRS) microscopy, and optical-photothermal infrared (O-PTIR) microscopy with multivariate data analysis, to investigate the biochemistry of brain hippocampus in situ using a mouse model of tauopathy (rTg4510). We observed a significant difference in the morphology and lipid content between transgenic (TG) and wild type (WT) samples. Immunohistochemical staining revealed some degree of microglia co-localisation with elevated lipids in the brain. These results provide new evidence of tauopathy-related dysfunction in a preclinical study at a subcellular level.
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Affiliation(s)
- Hao Meng
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Alicia Elliott
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Jessica Mansfield
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Michelle Bailey
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Mark Frogley
- Diamond Light Source, MIRIAM beamline B22, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Gianfelice Cinque
- Diamond Light Source, MIRIAM beamline B22, Harwell Science & Innovation Campus, Didcot, OX11 0DE, UK
| | - Julian Moger
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Nick Stone
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK
| | - Francesco Tamagnini
- School of Pharmacy, University of Reading, Reading, RG6 6UB, UK
- Centro Studi Biomedici, Università degli Studi della Repubblica di San Marino, Salita alla Rocca, 44 - 47890, San Marino Città, Republic of San Marino
| | - Francesca Palombo
- Department of Physics and Astronomy, University of Exeter, Exeter, EX4 4QL, UK.
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Martins DOS, Ruiz UEA, Santos IA, Oliveira IS, Guevara-Vega M, de Paiva REF, Abbehausen C, Sabino-Silva R, Corbi PP, Jardim ACG. Exploring the antiviral activities of the FDA-approved drug sulfadoxine and its derivatives against Chikungunya virus. Pharmacol Rep 2024; 76:1147-1159. [PMID: 39150661 DOI: 10.1007/s43440-024-00635-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND Currently, there is no antiviral licensed to treat chikungunya fever, a disease caused by the infection with Alphavirus chikungunya (CHIKV). Treatment is based on analgesic and anti-inflammatory drugs to relieve symptoms. Our study aimed to evaluate the antiviral activity of sulfadoxine (SFX), an FDA-approved drug, and its derivatives complexed with silver(I) (AgSFX), salicylaldehyde Schiff base (SFX-SL), and with both Ag and SL (AgSFX-SL) against CHIKV. METHODS The anti-CHIKV activity of SFX and its derivatives was investigated using BHK-21 cells infected with CHIKV-nanoluc, a marker virus-carrying nanoluciferase reporter. Dose-response and time of drug-addition assays were performed in order to assess the antiviral effects of the compounds, as well as in silico data and ATR-FTIR analysis for insights on their mechanisms of action. RESULTS The SFX inhibited 34% of CHIKV replication, while AgSFX, SFX-SL, and AgSFX-SL enhanced anti-CHIKV activity to 84%, 89%, and 95%, respectively. AgSFX, SFX-SL, and AgSFX-SL significantly decreased viral entry and post-entry to host cells, and the latter also protected cells against infection. Additionally, molecular docking calculations and ATR-FTIR analysis demonstrated interactions of SFX-SL, AgSFX, and AgSFX-SL with CHIKV. CONCLUSIONS Collectively, our findings suggest that the addition of metal ions and/or Schiff base to SFX improved its antiviral activity against CHIKV.
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Affiliation(s)
- Daniel Oliveira Silva Martins
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
- Institute of Bioscience, Language and Exact Sciences - IBILCE, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Uriel Enrique Aquino Ruiz
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | - Igor Andrade Santos
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | | | - Marco Guevara-Vega
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | | | - Camilla Abbehausen
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Robinson Sabino-Silva
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil
| | - Pedro Paulo Corbi
- Institute of Chemistry, University of Campinas - UNICAMP, Campinas, SP, Brazil
| | - Ana Carolina Gomes Jardim
- Institute of Biomedical Science - ICBIM, Federal University of Uberlândia - UFU, Avenida Amazonas, 4C- Room 216, Umuarama, Uberlândia, MG, CEP: 38405-302, Brazil.
- Institute of Bioscience, Language and Exact Sciences - IBILCE, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil.
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Chaudhary P, Verma A, Chaudhary S, Kumar M, Lin MF, Huang YC, Chen KL, Yadav BC. Design of a Humidity Sensor for a PPE Kit Using a Flexible Paper Substrate. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9602-9612. [PMID: 38651307 DOI: 10.1021/acs.langmuir.4c00366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The present work reports the rapid sweat detection inside a PPE kit using a flexible humidity sensor based on hydrothermally synthesized ZnO (zinc oxide) nanoflowers (ZNFs). Physical characterization of ZNFs was done using scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transmission infrared spectroscopy (FTIR), UV-visible, particle size analysis, Raman analysis, and X-ray photoelectron spectroscopy (XPS) analysis, and the hydrophilicity was investigated by using contact angle measurement. Fabrication of a flexible sensor was done by deposition on the paper substrate using the spin coating technique. It exhibited high sensitivity and low response and recovery times in the humidity range 10-95%RH. The sensor demonstrated the highest sensitivity of 296.70 nF/%RH within the humidity range 55-95%RH, and the rapid response and recovery times were also calculated and found as 5.10/1.70 s, respectively. The selectivity of the proposed sensor was also analyzed, and it is highly sensitive to humidity. The humidity sensing characteristics were theoretically witnessed in terms of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and electronic properties of sensing materials in ambient and humid conditions. These theoretical results are evidence of the interaction of ZnO with humidity. Overall, the present study provides a scope of architecture-enabled paper-based humidity sensors for the detection of sweat levels inside PPE kits for health workers.
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Affiliation(s)
- Priyanka Chaudhary
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Arpit Verma
- Nanomaterials and Sensors Research Laboratory, Department of Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025, India
| | - Sandeep Chaudhary
- Department of Mathematics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025, India
| | - Mahesh Kumar
- Department of Electrical Engineering, Indian Institute of Technology Jodhpur, Jodhpur 342011, India
| | - Meng-Fang Lin
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Yu-Ching Huang
- Department of Materials Engineering, Ming Chi University of Technology, New Taipei City 24301, Taiwan
| | - Kuen-Lin Chen
- Department of Physics, National Chung Hsing University, Taichung 40227, Taiwan
| | - B C Yadav
- Nanomaterials and Sensors Research Laboratory, Department of Physics, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh 226025, India
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Yin Y, Cui D, Chi Q, Xu H, Guan P, Zhang H, Jiao T, Wang X, Wang L, Sun H. Reactive oxygen species may be involved in the distinctive biological effects of different doses of 12C 6+ ion beams on Arabidopsis. FRONTIERS IN PLANT SCIENCE 2024; 14:1337640. [PMID: 38312361 PMCID: PMC10835405 DOI: 10.3389/fpls.2023.1337640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/31/2023] [Indexed: 02/06/2024]
Abstract
Introduction Heavy ion beam is a novel approach for crop mutagenesis with the advantage of high energy transfer line density and low repair effect after injury, however, little investigation on the biological effect on plant was performed. 50 Gy irradiation significantly stimulated the growth of Arabidopsis seedlings, as indicated by an increase in root and biomass, while 200 Gy irradiation significantly inhibited the growth of seedlings, causing a visible decrease in plant growth. Methods The Arabidopsis seeds were irradiated by 12C6+. Monte Carlo simulations were used to calculate the damage to seeds and particle trajectories by ion implantation. The seed epidermis received SEM detection and changes in its organic composition were detected using FTIR. Evidence of ROS and antioxidant systems were analyzed. RNA-seq and qPCR were used to detect changes in seedling transcript levels. Results and discussion Monte Carlo simulations revealed that high-dose irradiation causes various damage. Evidence of ROS and antioxidant systems implies that the emergence of phenotypes in plant cells may be associated with oxidative stress. Transcriptomic analysis of the seedlings demonstrated that 170 DEGs were present in the 50 Gy and 200 Gy groups and GO enrichment indicated that they were mainly associated with stress resistance and cell wall homeostasis. Further GO enrichment of DEGs unique to 50 Gy and 200 Gy revealed 58 50Gy-exclusive DEGs were enriched in response to oxidative stress and jasmonic acid entries, while 435 200 Gy-exclusive DEGs were enriched in relation to oxidative stress, organic cyclic compounds, and salicylic acid. This investigation advances our insight into the biological effects of heavy ion irradiation and the underlying mechanisms.
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Affiliation(s)
- Yue Yin
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Dongjie Cui
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Qing Chi
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Hangbo Xu
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Panfeng Guan
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
| | - Hanfeng Zhang
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Tao Jiao
- Asset Management Co., Ltd, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojie Wang
- School of Bioengineering, Xinxiang University, Xinxiang, China
| | - Lin Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hao Sun
- Henan Key Laboratory of Ion-beam Bioengineering, School of Physics and Microelectronics, Zhengzhou University, Zhengzhou, China
- State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- Sanya Institute, Zhengzhou University, Zhengzhou, China
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Jiang T, Duan J, Zhang Z, Xie B, Yang Z. Performance matching of common pesticides in banana plantations on the surface of banana leaves at different growth stages. PEST MANAGEMENT SCIENCE 2023; 79:5116-5129. [PMID: 37565694 DOI: 10.1002/ps.7713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND The effective deposition of pesticide droplets on a target leaf surface is critical for decreasing pesticide application rates. The wettability between the target leaf surface and the pesticide spray liquid should be investigated in depth, with the aim of enhancing the adhesion of pesticide solutions. The wetting and deposition behavior of pesticides on target leaves depends on the properties of the liquid and the physical and chemical properties of the leaves. The physical and chemical properties of leaves vary with growth stage. This study aims to investigate the wetting behavior of banana leaf surfaces at different stages. RESULTS The microstructures and chemical compositions of banana leaf surfaces at different stages were studied using modern methods. The surface structure of banana leaves exhibited a wide variety of characteristics at different growth stages, and the chemical composition changed marginally. The surface free energy (SFE) and polar and non-polar components of banana leaves at different growth stages were measured by examining the contact angles (CA) of different test solutions on the surface of banana leaves. Previous research has suggested that changes in the CA and SFE correlate with changes in leaf surface wettability. In general, the new upper leaves of banana trees are composed of polar components and exhibit hydrophobicity. Non-polar components become dominant as the leaf grows. The back surface of banana leaves was non-polar at all growth stages, with a trend that was opposite to that of the front surface. The critical surface tension of the banana leaf surface at different growth stages ranged from 7.83 to 24.22 mN m-1 , thus falling into the category of a low-energy surface. CONCLUSION The surface roughness and chemical characteristics of banana leaves affected the wettability of the leaf surface. Differences in the free energy and the polar and non-polar components of the leaf surface at were seen at different growth stages. This study provides a favorable reference for the rational control of pesticide spraying parameters and the enhancement of wetting and adhesion of the solution on banana leaf surfaces. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Tingting Jiang
- College of Engineering, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jieli Duan
- College of Engineering, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhihong Zhang
- College of Engineering, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Bowei Xie
- College of Engineering, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhou Yang
- College of Engineering, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
- School of Mechanical Engineering, Guangdong Ocean University, Zhanjiang, China
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Ali S, Naveed A, Hussain I, Qazi J. Diagnosis and monitoring of hepatocellular carcinoma in Hepatitis C virus patients using attenuated total reflection Fourier transform infrared spectroscopy. Photodiagnosis Photodyn Ther 2023; 43:103677. [PMID: 37390855 DOI: 10.1016/j.pdpdt.2023.103677] [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: 04/27/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
BACKGROUND Current diagnostic methods for assessment of hepatitis C virus related hepatocellular carcinoma and subsequent categorization of hepatocellular carcinoma into non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma, to establish appropriate treatment strategies, are costly, invasive and requires multiple screening steps. This demands alternative diagnostic approaches that are cost-effective, time-efficient, and minimally invasive, while maintaining their efficacy for screening of hepatitis c virus related hepatocellular carcinoma. In this study, we propose that attenuated total reflection Fourier transform infrared in conjunction with principal component analysis - linear discriminant analysis and support vector machine multivariate algorithms holds a potential as a sensitive tool for the detection of hepatitis C virus-related hepatocellular carcinoma and the subsequent categorization of hepatocellular carcinoma into non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma. METHODS Freeze-dried sera samples collected from 31 hepatitis c virus related hepatocellular carcinoma patients and 30 healthy individuals, were used to acquire mid-infrared absorbance spectra (3500-900 cm-1) using attenuated total reflection Fourier transform infrared. Chemometric machine learning techniques were utilized to build principal component analysis - linear discriminant analysis and support vector machine discriminant models for the spectral data of hepatocellular carcinoma patients and healthy individuals. Sensitivity, specificity, and external validation on blind samples were calculated. RESULTS Major variations were observed in the two spectral regions i.e., 3500-2800 and 1800-900 cm-1. IR spectral signatures of hepatocellular carcinoma were reliably different from healthy individuals. Principal component analysis - linear discriminant analysis and support vector machine models computed 100% accuracy for diagnosing hepatocellular carcinoma. To classify the non-angio-invasive hepatocellular carcinoma/ angio-invasive hepatocellular carcinoma status, diagnostic accuracy of 86.21% was achieved for principal component analysis - linear discriminant analysis. While the support vector machine showed a training accuracy of 98.28% and a cross-validation accuracy of 82.75%. External validation for support vector machine based classification observed 100% sensitivity and specificity for accurately classifying the freeze-dried sera samples for all categories. CONCLUSIONS We present the specific spectral signatures for non-angio-invasive hepatocellular carcinoma and angio-invasive hepatocellular carcinoma, which were prominently differentiated from healthy individuals. This study provides an initial insight into the potential of attenuated total reflection Fourier transform infrared to diagnose hepatitis C virus related hepatocellular carcinoma but also to further categorize into non-angio-invasive and angio-invasive hepatocellular carcinoma.
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Affiliation(s)
- Salmann Ali
- Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Ammara Naveed
- Department of gastroenterology and hepatology, Pakistan Kidney and Liver Institute, Lahore, Pakistan
| | - Irshad Hussain
- Department of Chemistry &Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), DHA, Lahore Cantt 54792, Pakistan
| | - Javaria Qazi
- Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.
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Mateus Pereira de Souza N, Hunter Machado B, Koche A, Beatriz Fernandes da Silva Furtado L, Becker D, Antonio Corbellini V, Rieger A. Detection of metabolic syndrome with ATR-FTIR spectroscopy and chemometrics in blood plasma. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122135. [PMID: 36442341 DOI: 10.1016/j.saa.2022.122135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/02/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
Metabolic Syndrome (MetS) is a constellation of 3 or more risk factor (abdominal obesity, high triglycerides, low HDL-c, high blood pressure, and elevated blood glucose) for atherosclerotic cardiovascular disease. Considering these systemic metabolic changes in the biochemical pathways of all biomolecules, Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy is a rapid, low-cost, and reagent-free alternative technique capable of identifying spectral biomarkers that differentiate subjects with MetS from control. In this study, plasma samples from 74 subjects (14 MetS, 60 control) were analyzed on the ATR-FTIR spectrophotometer. The objective was to differentiate subjects with MetS from control with supervised chemometrics modeling (Orthogonal Partial Least Squares-Discriminant Analysis, OPLS-DA). Additionally, the inflammatory status of subjects with MetS and control (supervised by C-reactive protein - CRP, leptin, and cell-free DNA - cfDNA) was verified. The OPLS-DA model achieved 100% sensitivity and specificity in cross-validation. For 1 latent variable (93.4% of variance), RMSECV < 0.002, PRESS CV < 0.0001, and R2 > 0.9999 was obtained. Significant spectrochemical differences (p < 0.05) were found between MetS and control subjects in the following biomolecular regions (cm-1): 1717-1703 [ν(CO) and δ(NH)], 1166-1137 [ν(C-OH) + ν(CO) and ν(CC) + δ(OH) + ν(CO)], 1113-1040 [ν(PO2-) and ν(C-OH)], and 1027-1008 [ν(CO) and v(CH2OH)]. In the OPLS-DA model loadings, amide I [1720-1600 cm-1, ν(CO)] and amide II [1570-1480 cm-1, δ(NH) + ν(CH)] had significantly greater weight than all other regions. There was a significant difference in inflammatory status between MetS patient and control (p < 0.05 for CRP and leptin, and p < 0.01 for cfDNA).
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Affiliation(s)
| | - Brenda Hunter Machado
- International Affairs, International University Centre, Santa Cruz do Sul, RS, Brazil.
| | - Andreia Koche
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil.
| | | | - Débora Becker
- Bachelor of Biological Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil
| | - Valeriano Antonio Corbellini
- Department of Sciences, Humanities and, Education, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
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Prada P, Brunel B, Moulin D, Rouillon L, Netter P, Loeuille D, Slimano F, Bouche O, Peyrin-Biroulet L, Jouzeau JY, Piot O. Identification of circulating biomarkers of Crohn's disease and spondyloarthritis using Fourier transform infrared spectroscopy. JOURNAL OF BIOPHOTONICS 2023; 16:e202200200. [PMID: 36112612 DOI: 10.1002/jbio.202200200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Crohn's disease (CD) and spondyloarthritis (SpA) are two inflammatory diseases sharing many common features (genetic polymorphism, armamentarium). Both diseases lack diagnostic markers of certainty. While the diagnosis of CD is made by a combination of clinical, and biological criteria, the diagnosis of SpA may take several years to be confirmed. Based on the hypothesis that CD and SpA alter the biochemical profile of plasma, the objective of this study was to evaluate the analytical capability of Fourier transform infrared spectroscopy (FTIR) in identifying spectral biomarkers. Plasma from 104 patients was analyzed. After data processing of the spectra by Extended Multiplicative Signal Correction and linear discriminant analysis, we demonstrated that it was possible to distinguish CD and SpA from controls with an accuracy of 97% and 85% respectively. Spectral differences were mainly associated with proteins and lipids. This study showed that FTIR analysis is efficient to identify plasma biosignatures specific to CD or SpA.
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Affiliation(s)
- Pierre Prada
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Benjamin Brunel
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, Besançon, France
| | - David Moulin
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Lise Rouillon
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Patrick Netter
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Damien Loeuille
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Florian Slimano
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Olivier Bouche
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Laurent Peyrin-Biroulet
- Département de Gastroentérologie, Hôpital Universitaire de Nancy-Brabois, Vandœuvre-lès-Nancy, France
| | - Jean-Yves Jouzeau
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Olivier Piot
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
- Plateforme d'Imagerie Cellulaire ou Tissulaire (PICT), Université de Reims Champagne-Ardenne, Reims, France
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Al-Naim AF, Sedky A, Afify N, Ibrahim SS. Structural, FTIR spectra and optical properties of pure and co-doped Zn 1-x-y Fe x M y O ceramics with (M = Cu, Ni) for plastic deformation and optoelectronic applications. APPLIED PHYSICS. A, MATERIALS SCIENCE & PROCESSING 2021; 127:840. [PMID: 34690444 PMCID: PMC8519334 DOI: 10.1007/s00339-021-04915-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/08/2021] [Indexed: 05/31/2023]
Abstract
We report here a considered novel study on the structural, FTIR spectra and optical properties of pure and co-doped Zn0.90-x Fe0.1M x O with ((M = Cu, Ni and (x = 0.00, 0.10) and (0.00 < y < 0.20)) at different sintering temperatures T s (T s = 850 °C for series I and 1000 °C series II). Although the ZnO wurtzite structure is conformed for all samples, some secondary lines with little intensity are formed. But the number of these lines is higher for series I than for series II. The (c/a) value and U-parameter are almost constant for all samples, while Zn-O bond length L is slightly increased. The porosity and crystallite size are decreased by Fe, and also for (Fe + Cu) samples, and their values for series I are lower than for series II. The residual stress is tensile for most samples. Interestingly, the Young's, rigid and bulk modulus, Poisson's ratio and Debye temperature, obtained from FTIR analysis, are increased by Fe addition with a further increase for Fe + Ni) samples for both series. A ductile nature is obtained for pure, Fe and (Fe + Cu) samples; whereas a brittle nature is approved for (Fe + Ni) samples. On the other hand, the energy gap (E g ), residual lattice dielectric constant (ε L ) and carrier density N are increased by Fe addition, followed by a further increase for (Fe + Cu) samples, while the vice is versa for the inter-atomic distance R. For example, E g was increased from 3.153 eV for pure ZnO to 3.974 eV for (Fe + Cu) samples (i.e., 0.821 eV more), while it was decreased to 2.851 eV for (Fe + Ni) samples (i.e., 0.302 eV less). A direct behavior is obtained between E g and both elastic modulus (Y, β), lattice and micro strains (ε L , ε m ), dislocation density (δ), residual stress (σ) and carrier density N, whereas a reverse behavior is obtained between E g and both crystallite size (D), porosity (PS) and inter-atomic distance (R) . These results are explained in terms of the generated blocked states of the conduction band as indicated by the Burstein Moss effect. These novel findings reveal that the co-doping has intense ZnO and moderate metal oxide modes in the ZnO matrix structure, which makes ZnO co-doped with (Fe + Cu) more suitable for gas sensors and optoelectronic devices. In contrast, ZnO co-doped with (Fe + Ni) samples is strongly recommended for altering plastic deformation. To our knowledge, the present investigation can be considered the first study and probably has never been discussed elsewhere, which highlights the present investigation.
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Affiliation(s)
- Abdullah F. Al-Naim
- Department of Physics, Faculty of Science, King Faisal University, P.O.B 400, Al-Hassa, 31982 Saudi Arabia
| | - A. Sedky
- Department of Physics, Faculty of Science, Assiut University, Assiut, 71516 Egypt
- Sphinx University, New Assiut City, Assiut, Egypt
| | - N. Afify
- Department of Physics, Faculty of Science, Assiut University, Assiut, 71516 Egypt
| | - S. S. Ibrahim
- Department of Physics, Faculty of Science, Cairo University, Giza, Egypt
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10
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Lukose J, Chidangil S, George SD. Optical technologies for the detection of viruses like COVID-19: Progress and prospects. Biosens Bioelectron 2021; 178:113004. [PMID: 33497877 PMCID: PMC7832448 DOI: 10.1016/j.bios.2021.113004] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023]
Abstract
The outbreak of life-threatening pandemic like COVID-19 necessitated the development of novel, rapid and cost-effective techniques that facilitate detection of viruses like SARS-CoV-2. The presently popular approach of a collection of samples using the nasopharyngeal swab method and subsequent detection of RNA using the real-time polymerase chain reaction suffers from false-positive results and a longer diagnostic time scale. Alternatively, various optical techniques namely optical sensing, spectroscopy, and imaging shows a great promise in virus detection. Herein, a comprehensive review of the various photonics technologies employed for virus detection, particularly the SARS-CoV family, is discussed. The state-of-art research activities in utilizing the photonics tools such as near-infrared spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, fluorescence-based techniques, super-resolution microscopy, surface plasmon resonance-based detection, for virus detection accounted extensively with an emphasis on coronavirus detection. Further, an account of emerging photonics technologies of SARS-CoV-2 detection and future possibilities is also explained. The progress in the field of optical techniques for virus detection unambiguously show a great promise in the development of rapid photonics-based devices for COVID-19 detection.
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Affiliation(s)
- Jijo Lukose
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, India; Centre of Excellence for Biophotonics, Manipal Academy of Higher Education, Manipal, 576 104, India
| | - Santhosh Chidangil
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, India; Centre of Excellence for Biophotonics, Manipal Academy of Higher Education, Manipal, 576 104, India
| | - Sajan D George
- Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, 576 104, India; Centre for Applied Nanosciences, Manipal Academy of Higher Education, Manipal, 576 104, India.
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11
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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 PMCID: PMC7960715 DOI: 10.1038/s41598-021-85371-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [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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12
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Moreau J, Bouzy P, Guillard J, Untereiner V, Garnotel R, Marchal A, Gobinet C, Terryn C, Sockalingum GD, Thiéfin G. Analysis of Hepatic Fibrosis Characteristics in Cirrhotic Patients with and without Hepatocellular Carcinoma by FTIR Spectral Imaging. Molecules 2020; 25:molecules25184092. [PMID: 32906799 PMCID: PMC7570752 DOI: 10.3390/molecules25184092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/31/2020] [Accepted: 09/04/2020] [Indexed: 12/12/2022] Open
Abstract
The evolution of cirrhosis is marked by quantitative and qualitative modifications of the fibrosis tissue and an increasing risk of complications such as hepatocellular carcinoma (HCC). Our purpose was to identify by FTIR imaging the spectral characteristics of hepatic fibrosis in cirrhotic patients with and without HCC. FTIR images were collected at projected pixel sizes of 25 and 2.7 μm from paraffinized hepatic tissues of five patients with uncomplicated cirrhosis and five cirrhotic patients with HCC and analyzed by k-means clustering. When compared to the adjacent histological section, the spectral clusters corresponding to hepatic fibrosis and regeneration nodules were easily identified. The fibrosis area estimated by FTIR imaging was correlated to that evaluated by digital image analysis of histological sections and was higher in patients with HCC compared to those without complications. Qualitative differences were also observed when fibrosis areas were specifically targeted at higher resolution. The partition in two clusters of the fibrosis tissue highlighted subtle differences in the spectral characteristics of the two groups of patients. These data show that the quantitative and qualitative changes of fibrosis tissue occurring during the course of cirrhosis are detectable by FTIR imaging, suggesting the possibility of subclassifying cirrhosis into different steps of severity.
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Affiliation(s)
- Johanna Moreau
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
| | - Pascaline Bouzy
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Julien Guillard
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), 51097 Reims Cedex, France; (V.U.); (C.T.)
| | - Roselyne Garnotel
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Laboratoire de Biochimie-Pharmacologie-Toxicologie, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
| | - Aude Marchal
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Anatomie et Cytologie Pathologique, Centre Hospitalier Universitaire de Reims, 51100 Reims, France
| | - Cyril Gobinet
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Christine Terryn
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), 51097 Reims Cedex, France; (V.U.); (C.T.)
| | - Ganesh D. Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
| | - Gérard Thiéfin
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; (J.M.); (P.B.); (J.G.); (R.G.); (A.M.); (C.G.); (G.D.S.)
- Service d’Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
- Correspondence: ; Tel.: +33-6-87517-344; Fax: +33-3-26788-836
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Bangaoil R, Santillan A, Angeles LM, Abanilla L, Lim A, Ramos MC, Fellizar A, Guevarra L, Albano PM. ATR-FTIR spectroscopy as adjunct method to the microscopic examination of hematoxylin and eosin-stained tissues in diagnosing lung cancer. PLoS One 2020; 15:e0233626. [PMID: 32469931 PMCID: PMC7259682 DOI: 10.1371/journal.pone.0233626] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/10/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer remains the leading cause of cancer-related death worldwide. Since prognosis and treatment outcomes rely on fast and accurate diagnosis, there is a need for more cost-effective, sensitive, and specific method for lung cancer detection. Thus, this study aimed to determine the ability of ATR-FTIR in discriminating malignant from benign lung tissues and evaluate its concordance with H&E staining. Three (3) 5μm-thick sections were cut from formalin fixed paraffin embedded (FFPE) cell or tissue blocks from patients with lung lesions. The outer sections were H&E-stained and sent to two (2) pathologists to confirm the histopathologic diagnosis. The inner section was deparaffinized by standard xylene method and then subjected to ATR-FTIR analysis. Distinct spectral profiles that distinguished (p<0.05) one sample from another, called the "fingerprint region", were observed in five (5) peak patterns representing the amides, lipids, and nucleic acids. Principal component analysis and hierarchical cluster analysis evidently clustered the benign from malignant tissues. ATR-FTIR showed 97.73% sensitivity, 92.45% specificity, 94.85% accuracy, 91.49% positive predictive value and 98.00% negative predictive value in discriminating benign from malignant lung tissue. Further, strong agreement was observed between histopathologic readings and ATR-FTIR analysis. This study shows the potential of ATR-FTIR spectroscopy as a potential adjunct method to the gold standard, the microscopic examination of hematoxylin and eosin (H&E)-stained tissues, in diagnosing lung cancer.
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Affiliation(s)
- Ruth Bangaoil
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- University of Santo Tomas Hospital, Manila, Philippines
| | - Abegail Santillan
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Lara Mae Angeles
- University of Santo Tomas Hospital, Manila, Philippines
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Lorenzo Abanilla
- Divine Word Hospital, Tacloban City, Northern Leyte, Philippines
| | - Antonio Lim
- Divine Word Hospital, Tacloban City, Northern Leyte, Philippines
| | - Ma. Cristina Ramos
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Mariano Marcos Memorial Hospital and Medical Center, Ilocos Norte, Philippines
| | - Allan Fellizar
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- College of Science, University of Santo Tomas, Manila, Philippines
| | - Leonardo Guevarra
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Pia Marie Albano
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Mariano Marcos Memorial Hospital and Medical Center, Ilocos Norte, Philippines
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14
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Evaluation of freeze-dried human sera as a novel approach for ATR-FTIR spectroscopic analysis as compared to conventionally used thin dry film sera. Biotechnol Lett 2019; 41:1355-1360. [DOI: 10.1007/s10529-019-02739-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/09/2019] [Indexed: 12/25/2022]
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15
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Rizvi A, Ahmed B, Zaidi A, Khan MS. Bioreduction of toxicity influenced by bioactive molecules secreted under metal stress by Azotobacter chroococcum. ECOTOXICOLOGY (LONDON, ENGLAND) 2019; 28:302-322. [PMID: 30758729 DOI: 10.1007/s10646-019-02023-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/30/2019] [Indexed: 06/09/2023]
Abstract
Heavy metal pollution destruct soil microbial compositions and functions, plant's performance and subsequently human health. Culturable microbes among many metal abatement strategies are considered inexpensive, viable and environmentally safe. In this study, nitrogen fixing bacterial strain CAZ3 recovered from chilli rhizosphere tolerated 100, 1000 and 1200 µg mL-1 of cadmium, chromium and nickel, respectively and was identified as Azotobacter chroococcum by 16S rDNA sequence analysis. Under metal stress, cellular morphology of A. chroococcum observed under SEM was found distorted and shrinkage of cells was noticed when grown with 50 µg mL-1 of Cd (cell size 1.7 µm) and 100 of µg mL-1 Ni (cell size 1.3 µm) compared to untreated control (cell size 1.8 µm). In the presence of 100 µg mL-1 of Cr, cells became elongated and measured 1.9 µm in size. Location of metals inside the cells was revealed by EDX. A dose dependent growth arrest and consequently the death of A. chroococcum cells was revealed under CLSM. A. chroococcum CAZ3 secreted 320, 353 and 133 µg EPS mL-1 when grown with 100 µg mL-1 each of Cd, Cr and Ni, respectively. The EDX revealed the presence of 0.4, 0.07 and 0.24% of Cd, Cr and Ni, respectively within EPS extracted from metal treated cells. Moreover, a dark brown pigment (melanin) secreted by A. chroococcum cells under metal pressure displayed tremendous metal chelating activity. The EDX spectra of melanin extracted from metal treated cells of A. chroococcum CAZ3 displayed 0.53, 0.22 and 0.12% accumulation of Cd, Cr and Ni, respectively. The FT-IR spectra of EPS and melanin demonstrated stretching vibrations and variations in surface functional groups of bacterial cells. The C-H stretching of CH3 in fatty acids and CH2 groups, stretching of N-H bond of proteins and O-H bond of hydroxyl groups caused the shifting of peaks in the EPS spectra. Similar stretching vibrations were recorded in metal treated melanin which involved CHO, alkyl, carboxylate and alkene groups resulting in significant peak shifts. Nuclear magnetic resonance (NMR) spectrum of EPS extracted from A. chroococcum CAZ3 revealed apparent peak signals at 4.717, 9.497, 9.369 and 9.242 ppm. However, 1H NMR peaks were poorly resolved due largely to the impurity/viscosity of the EPS. The entrapment of metals by EPS and melanin was confirmed by EDX. Also, the induction and excretion of variable amounts of metallothioneins (MTs) by A. chroococcum under metal pressure was interesting. Conclusively, the present findings establish- (i) cellular damage due to Cd, Cr and Ni and (ii) role of EPS, melanin and MTs in adsorption/complexation and concurrently the removal of heavy metals. Considering these, A. chroococcum can be promoted as a promising candidate for supplying N efficiently to plants and protecting plants from metal toxicity while growing under metal stressed environment.
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Affiliation(s)
- Asfa Rizvi
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, UP, 202002, India.
| | - Bilal Ahmed
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Almas Zaidi
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Mohd Saghir Khan
- Faculty of Agricultural Sciences, Department of Agricultural Microbiology, Aligarh Muslim University, Aligarh, UP, 202002, India
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16
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Marques V, Cunha B, Couto A, Sampaio P, Fonseca LP, Aleixo S, Calado CRC. Characterization of gastric cells infection by diverse Helicobacter pylori strains through Fourier-transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 210:193-202. [PMID: 30453195 DOI: 10.1016/j.saa.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
The infection of Helicobacter pylori, covering 50% of the world-population, leads to diverse gastric diseases as ulcers and cancer along the life-time of the human host. To promote the discovery of biomarkers of bacterial infection, in the present work, Fourier-transform infrared spectra were acquired from adenocarcinoma gastric cells, incubated with H. pylori strains presenting different genotypes concerning the virulent factors cytotoxin associated gene A and vacuolating cytotoxin A. Defined absorbance ratios were evaluated by diverse methods of statistical inference, according to the fulfillment of the tests assumptions. It was possible to define from the gastric cells, diverse absorbance ratios enabling to discriminate: i) The infection; ii) the bacteria genotype; and iii) the gastric disease of the patients from which the bacteria were isolated. These biomarkers could fasten the knowledge of the complex infection process while promoting a platform for a new diagnostic method, rapid but also specific and sensitive towards the diagnosis of both infection and bacterial virulence.
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Affiliation(s)
- Vanda Marques
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Bernardo Cunha
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Andreia Couto
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Pedro Sampaio
- Faculty of Engineering, Lusophone University of Humanities and Technology, Campo Grande, 376, 1749-019 Lisbon, Portugal
| | - Luís P Fonseca
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sandra Aleixo
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Cecília R C Calado
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal.
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Damgaard IB, Riau AK, Liu YC, Tey ML, Yam GHF, Mehta JS. Reshaping and Customization of SMILE-Derived Biological Lenticules for Intrastromal Implantation. Invest Ophthalmol Vis Sci 2019; 59:2555-2563. [PMID: 29847663 DOI: 10.1167/iovs.17-23427] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To evaluate the feasibility of excimer laser reshaping of biological lenticules available after small incision lenticule extraction (SMILE). Methods Fresh and cryopreserved SMILE-derived human lenticules underwent excimer laser ablation for stromal reshaping. The treatment effects in the lasered group were compared with the nonlasered group with respect to changes in surface functional groups (by Fourier transform infrared spectroscopy [FTIR]) and surface morphology (by scanning electron microscopy [SEM] and atomic force microscopy [AFM]). Ten SMILE-derived porcine lenticules, five nonlasered (107-μm thick, -6 diopter [D] spherical power) and five excimer lasered (50% thickness reduction), were implanted into a 120-μm stromal pocket of 10 porcine eyes. Corneal thickness and topography were assessed before and after implantation. Results FTIR illustrated prominent changes in the lipid profile. The collagen structure was also affected by the laser treatment but to a lesser extent. SEM exhibited a more regular surface for the lasered lenticules, confirmed by the lower mean Rz value (290.1 ± 96.1 nm vs. 380.9 ± 92.6 nm, P = 0.045) on AFM. The lasered porcine lenticules were thinner than the nonlasered controls during overhydration (132 ± 26 μm vs. 233 ± 23 μm, P < 0.001) and after 5 hours in a moist chamber (46 ± 3 μm vs. 57 ± 3 μm, P < 0.001). After implantation, the nonlasered group showed a tendency toward a greater increase in axial keratometry (6.63 ± 2.17 D vs. 5.60 ± 3.79 D, P = 0.613) and elevation (18.6 ± 15.4 vs. 15.2 ± 5.5, P = 0.656) than the lasered group. Conclusions Excimer laser ablation may be feasible for thinning and reshaping of SMILE-derived lenticules before reimplantation or allogenic transplantation. However, controlled lenticule dehydration before ablation is necessary in order to allow stromal thinning.
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Affiliation(s)
- Iben Bach Damgaard
- Department of Ophthalmology, Aarhus University Hospital, Aarhus, Denmark.,Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore
| | - Andri Kartasasmita Riau
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore.,School of Materials Science and Engineering, Nanyang Technological University, Singapore
| | - Yu-Chi Liu
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore.,Singapore National Eye Centre, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore
| | - Min Li Tey
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gary Hin-Fai Yam
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore
| | - Jodhbir Singh Mehta
- Tissue Engineering and Stem Cell Group, Singapore Eye Research Institute, Singapore.,School of Materials Science and Engineering, Nanyang Technological University, Singapore.,Singapore National Eye Centre, Singapore.,Ophthalmology and Visual Sciences Academic Clinical Programme, Duke-NUS Graduate Medical School, Singapore
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18
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Muhammad W, Ullah N, Haroon M, Abbasi BH. Optical, morphological and biological analysis of zinc oxide nanoparticles (ZnO NPs) using Papaver somniferum L. RSC Adv 2019; 9:29541-29548. [PMID: 35531532 PMCID: PMC9071912 DOI: 10.1039/c9ra04424h] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
Biogenic synthesis of ZnO-NPs using P. somniferum.
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Affiliation(s)
- Wali Muhammad
- Department of Biotechnology
- Quaid-i-Azam University
- Islamabad
- Pakistan
| | - Naimat Ullah
- Department of Chemistry
- Quaid-i-Azam University
- Islamabad
- Pakistan
| | - Muhammad Haroon
- Department of Biotechnology
- Quaid-i-Azam University
- Islamabad
- Pakistan
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19
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Gavgiotaki E, Filippidis G, Markomanolaki H, Kenanakis G, Agelaki S, Georgoulias V, Athanassakis I. Distinction between breast cancer cell subtypes using third harmonic generation microscopy. JOURNAL OF BIOPHOTONICS 2017; 10:1152-1162. [PMID: 27753229 DOI: 10.1002/jbio.201600173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/10/2016] [Accepted: 09/30/2016] [Indexed: 06/06/2023]
Abstract
Third Harmonic Generation (THG) microscopy as a non-invasive, label free imaging methodology, allows linkage of lipid profiles with various breast cancer cells. The collected THG signal arise mostly from the lipid droplets and the membrane lipid bilayer. Quantification of THG signal can accurately distinguish HER2-positive cells. Further analysis using Fourier transform infrared (FTIR) spectra reveals cancer-specific profiles, correlating lipid raft-corresponding spectra to THG signal, associating thus THG to chemical information. THG imaging of a cancer cell.
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Affiliation(s)
- Evangelia Gavgiotaki
- Institute of Electronic Structure and Laser, Foundation for Research and Technology, Heraklion, 71110, Crete, Greece
- Medical School, University of Crete, Heraklion, 71003, Crete, Greece
| | - George Filippidis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology, Heraklion, 71110, Crete, Greece
| | | | - George Kenanakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology, Heraklion, 71110, Crete, Greece
| | - Sofia Agelaki
- Medical School, University of Crete, Heraklion, 71003, Crete, Greece
| | | | - Irene Athanassakis
- Department of Biology, University of Crete, Heraklion, 71409, Crete, Greece
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High-throughput FTIR-based bioprocess analysis of recombinant cyprosin production. ACTA ACUST UNITED AC 2017; 44:49-61. [DOI: 10.1007/s10295-016-1865-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/30/2016] [Indexed: 10/20/2022]
Abstract
Abstract
To increase the knowledge of the recombinant cyprosin production process in Saccharomyces cerevisiae cultures, it is relevant to implement efficient bioprocess monitoring techniques. The present work focuses on the implementation of a mid-infrared (MIR) spectroscopy-based tool for monitoring the recombinant culture in a rapid, economic, and high-throughput (using a microplate system) mode. Multivariate data analysis on the MIR spectra of culture samples was conducted. Principal component analysis (PCA) enabled capturing the general metabolic status of the yeast cells, as replicated samples appear grouped together in the score plot and groups of culture samples according to the main growth phase can be clearly distinguished. The PCA-loading vectors also revealed spectral regions, and the corresponding chemical functional groups and biomolecules that mostly contributed for the cell biomolecular fingerprint associated with the culture growth phase. These data were corroborated by the analysis of the samples’ second derivative spectra. Partial least square (PLS) regression models built based on the MIR spectra showed high predictive ability for estimating the bioprocess critical variables: biomass (R2 = 0.99, RMSEP 2.8%); cyprosin activity (R2 = 0.98, RMSEP 3.9%); glucose (R2 = 0.93, RMSECV 7.2%); galactose (R2 = 0.97, RMSEP 4.6%); ethanol (R2 = 0.97, RMSEP 5.3%); and acetate (R2 = 0.95, RMSEP 7.0%). In conclusion, high-throughput MIR spectroscopy and multivariate data analysis were effective in identifying the main growth phases and specific cyprosin production phases along the yeast culture as well as in quantifying the critical variables of the process. This knowledge will promote future process optimization and control the recombinant cyprosin bioprocess according to Quality by Design framework.
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Elshemey WM, Ismail AM, Elbialy NS. Molecular-Level Characterization of Normal, Benign, and Malignant Breast Tissues Using FTIR Spectroscopy. J Med Biol Eng 2016. [DOI: 10.1007/s40846-016-0133-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Gurbanov R, Bilgin M, Severcan F. Restoring effect of selenium on the molecular content, structure and fluidity of diabetic rat kidney brush border cell membrane. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:845-54. [DOI: 10.1016/j.bbamem.2016.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 02/02/2023]
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Lima CA, Goulart VP, Correa L, Zezell DM. Using Fourier transform infrared spectroscopy to evaluate biological effects induced by photodynamic therapy. Lasers Surg Med 2016; 48:538-45. [DOI: 10.1002/lsm.22473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2015] [Indexed: 12/16/2022]
Affiliation(s)
- Cassio A. Lima
- Instituto de Pesquisas Energéticas e Nucleares; IPEN - CNEN/SP; Universidade de Sao Paulo; Sao Paulo SP 05508 000 Brazil
| | - Viviane P. Goulart
- Instituto de Pesquisas Energéticas e Nucleares; IPEN - CNEN/SP; Universidade de Sao Paulo; Sao Paulo SP 05508 000 Brazil
| | - Luciana Correa
- Faculdade de Odontologia; Universidade de São Paulo; São Paulo SP 05508 000 Brazil
| | - Denise M. Zezell
- Instituto de Pesquisas Energéticas e Nucleares; IPEN - CNEN/SP; Universidade de Sao Paulo; Sao Paulo SP 05508 000 Brazil
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Romih T, Jemec A, Novak S, Vaccari L, Ferraris P, Šimon M, Kos M, Susič R, Kogej K, Zupanc J, Drobne D. FTIR microscopy reveals distinct biomolecular profile of crustacean digestive glands upon subtoxic exposure to ZnO nanoparticles. Nanotoxicology 2015; 10:462-70. [DOI: 10.3109/17435390.2015.1078853] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Rosa F, Sales KC, Cunha BR, Couto A, Lopes MB, Calado CRC. A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses. Anal Bioanal Chem 2015; 407:8097-108. [PMID: 26329279 DOI: 10.1007/s00216-015-8983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/29/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022]
Abstract
Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R (2) ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R (2) = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.
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Affiliation(s)
- Filipa Rosa
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Kevin C Sales
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Bernardo R Cunha
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Andreia Couto
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Marta B Lopes
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal.,Instituto de Telecomunicações, Instituto Superior Técnico, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
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Sales KC, Rosa F, Sampaio PN, Fonseca LP, Lopes MB, Calado CRC. In situ near-infrared (NIR) versus high-throughput mid-infrared (MIR) spectroscopy to monitor biopharmaceutical production. APPLIED SPECTROSCOPY 2015; 69:760-772. [PMID: 25955848 DOI: 10.1366/14-07588] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The development of biopharmaceutical manufacturing processes presents critical constraints, with the major constraint being that living cells synthesize these molecules, presenting inherent behavior variability due to their high sensitivity to small fluctuations in the cultivation environment. To speed up the development process and to control this critical manufacturing step, it is relevant to develop high-throughput and in situ monitoring techniques, respectively. Here, high-throughput mid-infrared (MIR) spectral analysis of dehydrated cell pellets and in situ near-infrared (NIR) spectral analysis of the whole culture broth were compared to monitor plasmid production in recombinant Escherichia coli cultures. Good partial least squares (PLS) regression models were built, either based on MIR or NIR spectral data, yielding high coefficients of determination (R(2)) and low predictive errors (root mean square error, or RMSE) to estimate host cell growth, plasmid production, carbon source consumption (glucose and glycerol), and by-product acetate production and consumption. The predictive errors for biomass, plasmid, glucose, glycerol, and acetate based on MIR data were 0.7 g/L, 9 mg/L, 0.3 g/L, 0.4 g/L, and 0.4 g/L, respectively, whereas for NIR data the predictive errors obtained were 0.4 g/L, 8 mg/L, 0.3 g/L, 0.2 g/L, and 0.4 g/L, respectively. The models obtained are robust as they are valid for cultivations conducted with different media compositions and with different cultivation strategies (batch and fed-batch). Besides being conducted in situ with a sterilized fiber optic probe, NIR spectroscopy allows building PLS models for estimating plasmid, glucose, and acetate that are as accurate as those obtained from the high-throughput MIR setup, and better models for estimating biomass and glycerol, yielding a decrease in 57 and 50% of the RMSE, respectively, compared to the MIR setup. However, MIR spectroscopy could be a valid alternative in the case of optimization protocols, due to possible space constraints or high costs associated with the use of multi-fiber optic probes for multi-bioreactors. In this case, MIR could be conducted in a high-throughput manner, analyzing hundreds of culture samples in a rapid and automatic mode.
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Affiliation(s)
- Kevin C Sales
- Engineering Faculty, Catholic University of Portugal, Estrada Octávio Pato, 2635-631, Rio de Mouro, Portugal
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Pénicaud C, Landaud S, Jamme F, Talbot P, Bouix M, Ghorbal S, Fonseca F. Physiological and biochemical responses of Yarrowia lipolytica to dehydration induced by air-drying and freezing. PLoS One 2014; 9:e111138. [PMID: 25350121 PMCID: PMC4211883 DOI: 10.1371/journal.pone.0111138] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 09/29/2014] [Indexed: 11/23/2022] Open
Abstract
Organisms that can withstand anhydrobiosis possess the unique ability to temporarily and reversibly suspend their metabolism for the periods when they live in a dehydrated state. However, the mechanisms underlying the cell's ability to tolerate dehydration are far from being fully understood. The objective of this study was to highlight, for the first time, the cellular damage to Yarrowia lipolytica as a result of dehydration induced by drying/rehydration and freezing/thawing. Cellular response was evaluated through cell cultivability determined by plate counts, esterase activity and membrane integrity assessed by flow cytometry, and the biochemical composition of cells as determined by FT-IR spectroscopy. The effects of the harvesting time (in the log or stationary phase) and of the addition of a protective molecule, trehalose, were investigated. All freshly harvested cells exhibited esterase activity and no alteration of membrane integrity. Cells freshly harvested in the stationary phase presented spectral contributions suggesting lower nucleic acid content and thicker cell walls, as well as longer lipid chains than cells harvested in the log phase. Moreover, it was found that drying/rehydration induced cell plasma membrane permeabilization, loss of esterase activity with concomitant protein denaturation, wall damage and oxidation of nucleic acids. Plasma membrane permeabilization and loss of esterase activity could be reduced by harvesting in the stationary phase and/or with trehalose addition. Protein denaturation and wall damage could be reduced by harvesting in the stationary phase. In addition, it was shown that measurements of loss of membrane integrity and preservation of esterase activity were suitable indicators of loss and preservation of cultivability, respectively. Conversely, no clear effect of freezing/thawing could be observed, probably because of the favorable operating conditions applied. These results give insights into Y. lipolytica mechanisms of cellular response to dehydration and provide a basis to better understand its ability to tolerate anhydrobiosis.
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Affiliation(s)
- Caroline Pénicaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sophie Landaud
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | | | - Pauline Talbot
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Marielle Bouix
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Sarrah Ghorbal
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
| | - Fernanda Fonseca
- INRA, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
- AgroParisTech, UMR782 Génie et Microbiologie des Procédés Alimentaires, Thiverval-Grignon, France
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Skotti E, Kountouri S, Bouchagier P, Tsitsigiannis DI, Polissiou M, Tarantilis PA. FTIR spectroscopic evaluation of changes in the cellular biochemical composition of the phytopathogenic fungus Alternaria alternata induced by extracts of some Greek medicinal and aromatic plants. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 127:463-472. [PMID: 24657421 DOI: 10.1016/j.saa.2014.02.113] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2013] [Revised: 02/21/2014] [Accepted: 02/26/2014] [Indexed: 06/03/2023]
Abstract
In this study, the biological activity of aquatic extracts of selected Greek medicinal and aromatic plants to the phytopathogenic fungus Alternaria alternata was investigated. Lamiaceae species (Hyssopus officinalis L., Melissa officinalis L., Origanum dictamnus L., Origanum vulgare L. and Salvia officinalis L.) were found to enhance significantly the mycelium growth whereas Crocus sativus appears to inhibit it slightly. M. officinalis and S. officinalis caused the highest stimulation in mycelium growth (+97%) and conidia production (+65%) respectively. In order to further investigate the bioactivity of plant extracts to A. alternata, we employed Fourier Transform Infrared Spectroscopy (FTIR). Differences of original spectra were assigned mainly to amides of proteins. The second derivative transformation of spectra revealed changes in spectral regions corresponding to absorptions of the major cellular constituents such as cell membrane and proteins. Principal component analysis of the second derivative transformed spectra confirmed that fatty acids of the cell membranes, amides of proteins and polysaccharides of the cell wall had the major contribution to data variation. FTIR band area ratios were found to correlate with fungal mycelium growth.
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Affiliation(s)
- Efstathia Skotti
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Sophia Kountouri
- Laboratory of Phytopathology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Pavlos Bouchagier
- Department of Food Technology, Technological Educational Institute of Ionian Islands, GR 28100 Kefallonia, Greece
| | - Dimitrios I Tsitsigiannis
- Laboratory of Phytopathology, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Moschos Polissiou
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Petros A Tarantilis
- Laboratory of Chemistry, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece.
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Giorgini E, Balercia P, Conti C, Ferraris P, Sabbatini S, Rubini C, Tosi G. Insights on diagnosis of oral cavity pathologies by infrared spectroscopy: A review. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.08.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ye D, Tanthanuch W, Thumanu K, Sangmalee A, Parnpai R, Heraud P. Discrimination of functional hepatocytes derived from mesenchymal stem cells using FTIR microspectroscopy. Analyst 2013; 137:4774-84. [PMID: 22946081 DOI: 10.1039/c2an35329f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Functional hepatocytes differentiated in vitro from mesenchymal stem cells (MSCs) need to be fully characterized before they could be applied as a therapy to treat liver disease. Here, we employed Fourier Transform Infrared (FTIR) microspectroscopy to investigate the characteristics of hepatocyte-like cells derived from rat bone marrow mesenchymal stem cells (rBM-MSCs) by detecting changes in macromolecular composition occurring during the hepatogenesis process. Partial Least Squares Discriminant Analysis (PLS-DA) enabled us to discriminate undifferentiated rBM-MSCs, and early, mid-stage and late stage rBM-MSCs derived hepatocytes by their characteristic FTIR "spectroscopic signatures". The predominant spectroscopic changes responsible for this discrimination were changes in FTIR absorbance bands at: 3012 cm(-1) (cis C[double bond, length as m-dash]C stretch from unsaturated lipids), 2952 cm(-1) (ν(as)CH(3) from lipids), 2854 cm(-1) (ν(s)CH(2) from lipids) and 1722 cm(-1) (C[double bond, length as m-dash]O stretching from lipids), which were associated with triglyceride and unsaturated fatty acid accumulation in the hepatocyte-like cells occurring during differentiation. Based on these findings, rBM-MSCs derived hepatocytes are characterized by high lipid content which facilitates a means of identifying hepatocytes from their stem cells progenitors by using FTIR microspectroscopy. Other complex changes in spectral bands assigned to proteins and nucleic acids were observed during hepatocyte differentiation indicating that mRNA translation was taking place producing proteins related to the formation of the new hepatocyte-like phenotype, which was corroborated by immunohistochemistry. The results show FTIR microspectroscopy combined with bioinformatic modeling constitutes a powerful new phenotypic-based methodology for monitoring and characterization of the process of stem cell differentiation leading to the formation of hepatocytes, providing complementary information to existing methodologies such as immunohistochemistry and gene analysis, but having advantages of being reagent-free and non-destructive of the sample.
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Affiliation(s)
- Danna Ye
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Oral cancer diagnostics based on infrared spectral markers and wax physisorption kinetics. Anal Bioanal Chem 2013; 405:1995-2007. [PMID: 23318761 DOI: 10.1007/s00216-012-6625-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 11/13/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
Abstract
Infrared microspectroscopy is an emerging approach for disease analysis owing to its capability for in situ chemical characterization of pathological processes. Synchrotron-based infrared microspectroscopy (SR-IMS) provides ultra-high spatial resolution for profiling biochemical events associated with disease progression. Spectral alterations were observed in cultured oral cells derived from healthy, precancerous, primary, and metastatic cancers. An innovative wax-physisorption-based kinetic FTIR imaging method for the detection of oral precancer and cancer was demonstrated successfully. The approach is based on determining the residual amount of paraffin wax (C(25)H(52)) or beeswax (C(46)H(92)O(2)) on a sample surface after xylene washing. This amount is used as a signpost of the degree of physisorption that altered during malignant transformation. The results of linear discriminant analysis (LDA) of oral cell lines indicated that the methylene (CH(2)) and methyl group (CH(3)) stretching vibrations in the range of 3,000-2,800 cm(-1) have the highest accuracy rate (89.6 %) to discriminate the healthy keratinocytes (NHOK) from cancer cells. The results of wax-physisorption-based FTIR imaging showed a stronger physisorption with beeswax in oral precancerous and cancer cells as compared with that of NHOK, which showed a strong capability with paraffin wax. The infrared kinetic study of oral cavity tissue showed a consistency in the wax physisorption of the cell lines. On the basis of our findings, these results show the potential use of wax-physisorption-based kinetic FTIR imaging for the early screening of oral cancer lesions and the chemical changes during oral carcinogenesis.
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Ostrovsky E, Zelig U, Gusakova I, Ariad S, Mordechai S, Nisky I, Kapilushnik J. Detection of cancer using advanced computerized analysis of infrared spectra of peripheral blood. IEEE Trans Biomed Eng 2012. [PMID: 23193226 DOI: 10.1109/tbme.2012.2226882] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed a novel approach for detection of cancer based on biochemical analysis of peripheral blood plasma using Fourier transform infrared spectroscopy. This approach has proven to be quick, safe, minimal invasive, and effective. Our approach recognizes any signs of solid tumor presence, regardless of location in the body or cancer type by measuring a spectrum that gives information regarding the total molecular composition and structure of the peripheral blood samples. The analysis includes clinically relevant preprocessing and feature extraction with principal component analysis, and uses Fisher's linear discriminant analysis to classify between cancer patients and healthy controls. We evaluated our method with leave-one-out cross validation and were able to establish sensitivity of 93.33%, specificity of 87.8%, and overall accuracy of 90.7%. Using our method for cancer detection should result in fewer unnecessary invasive procedures and yield fast detection of solid tumors.
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Affiliation(s)
- Ela Ostrovsky
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
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Lu X, Wang J, Al-Qadiri HM, Ross CF, Powers JR, Tang J, Rasco BA. Determination of total phenolic content and antioxidant capacity of onion (Allium cepa) and shallot (Allium oschaninii) using infrared spectroscopy. Food Chem 2011; 129:637-644. [PMID: 30634280 DOI: 10.1016/j.foodchem.2011.04.105] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 01/07/2011] [Accepted: 04/29/2011] [Indexed: 10/18/2022]
Abstract
Total phenolic content (TPC) and total antioxidant capacity (TAC) of four onion varieties (red, white, yellow and sweet) and shallot from selected locations (Washington, Idaho, Oregon, Texas and Georgia) were determined using Fourier transform infrared (FT-IR) spectroscopy (4000-400cm-1). The Folin-Ciocalteu (F-C) assay was used to quantify TPC and three assays were used to determine TAC, including 2,2-diphenyl-picrylhydrazyl (DPPH) assay, Trolox equivalent antioxidant capacity (TEAC) assay and ferric reducing antioxidant power (FRAP) assay. Partial least squares regression (PLSR) with cross-validation (leave-one-out) was conducted on onion and shallot extracts (n=200) and their corresponding F-C, DPPH, TEAC and FRAP values were employed to obtain four independent calibration models for predicting TPC and TAC for the extracts. Spectra from an extra 19 independent extracts were used as an external validation set for prediction. A correlation of r>0.95 was obtained between FT-IR predicted and reference values (by F-C, DPPH, TEAC and FRAP assay) with standard errors of calibration (SEC) and standard errors of cross-validation (SECV) less than 2.85, 0.35 and 0.45μmolTrolox/g FW of extracts for TEAC, FRAP and DPPH assay, respectively; and 0.36mggallic acid/g FW of extracts for the F-C assay. In addition, cluster analysis (principal component analysis (PCA)) and discriminant function analysis (DFA) could differentiate varieties of onions and shallot based upon infrared spectral features. Loading plots for the various chemometrics models indicated that hydroxyl and phenolic functional groups were most closely correlated with antioxidant capacity. The use of mid-infrared spectroscopy to predict the total antioxidant capacity of vegetables provides a rapid and precise alternative to traditional wet chemistry analysis.
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Affiliation(s)
- Xiaonan Lu
- School of Food Science, Washington State University, P.O. Box 646376, Pullman, WA 99163, USA
| | - Jun Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, PR China
| | - Hamzah M Al-Qadiri
- Department of Nutrition and Food Technology, The University of Jordan, Amman 11942, Jordan
| | - Carolyn F Ross
- School of Food Science, Washington State University, P.O. Box 646376, Pullman, WA 99163, USA
| | - Joseph R Powers
- School of Food Science, Washington State University, P.O. Box 646376, Pullman, WA 99163, USA
| | - Juming Tang
- Department of Biological System Engineering, Washington State University, Pullman, WA 99163, USA
| | - Barbara A Rasco
- School of Food Science, Washington State University, P.O. Box 646376, Pullman, WA 99163, USA.
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Khanmohammadi M, Ansari MA, Garmarudi AB, Hassanzadeh G, Garoosi G. Cancer Diagnosis by Discrimination between Normal and Malignant Human Blood Samples Using Attenuated Total Reflectance-Fourier Transform Infrared Spectroscopy. Cancer Invest 2009; 25:397-404. [PMID: 17882650 DOI: 10.1080/02770900701512555] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
FTIR spectroscopy is a common technique for cancer diagnosis. Applied tissue samples are heterogeneous and may be damaged in preparation procedures. Easier sampling, more available samples and also easier process with assured results would be interesting. Whole blood samples include all of these qualifications and our hypothesis was the bio-molecular changes in blood which manifest themselves in different optical signatures, detectable by FTIR spectroscopy. Noncancerous blood samples were differentiated from cancerous ones using ATR-FTIR spectroscopy and LDA classification method. Procedure was 100 percent and 90 percent accurate in prediction of cancerous or noncancerous situation for 33 known and 10 unknown samples, respectively.
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Affiliation(s)
- M Khanmohammadi
- Department of Chemistry, Faculty of Science, Imam Khomeini International University, Qazvin, Iran.
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35
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Monitoring of viral cancer progression using FTIR microscopy: A comparative study of intact cells and tissues. Biochim Biophys Acta Gen Subj 2008; 1780:1038-46. [DOI: 10.1016/j.bbagen.2008.05.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 05/22/2008] [Accepted: 05/22/2008] [Indexed: 11/21/2022]
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36
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HAMMODY Z, HULEIHEL M, SALMAN A, ARGOV S, MOREH R, KATZIR A, MORDECHAI S. Potential of ‘flat’ fibre evanescent wave spectroscopy to discriminate between normal and malignant cells in vitro. J Microsc 2007; 228:200-10. [DOI: 10.1111/j.1365-2818.2007.01840.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Erukhimovitch V, Talyshinsky M, Souprun Y, Huleihel M. Spectroscopic Characterization of Human and Mouse Primary Cells, Cell Lines and Malignant Cells¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0760446scoham2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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38
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Bogomolny E, Huleihel M, Suproun Y, Sahu RK, Mordechai S. Early spectral changes of cellular malignant transformation using Fourier transform infrared microspectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2007; 12:024003. [PMID: 17477718 DOI: 10.1117/1.2717186] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Fourier transform infrared microspectroscopy (FTIR-MSP) is potentially a powerful analytical method for identifying the spectral properties of biological activity in cells. The goal of the present research is the implementation of FTIR-MSP to study early spectral changes accompanying malignant transformation of cells. As a model system, cells in culture are infected by the murine sarcoma virus (MuSV), which induces malignant transformation. The spectral measurements are taken at various postinfection time intervals. To follow up systematically the progress of the spectral changes at early stages of cell transformation, it is essential first to determine and validate consistent and significant spectral parameters (biomarkers), which can evidently discriminate between normal and cancerous cells. Early stages of cell transformation are classified by an array of spectral biomarkers utilizing cluster analysis and discriminant classification function techniques. The classifications indicate that the first spectral changes are detectable much earlier than the first morphological signs of cell transformation. Our results point out that the first spectral signs of malignant transformation are observed on the first and third day of postinfection (PI) (for NIH/3T3 and MEF cell cultures, respectively), while the first visible morphological alterations are observed only on the third and seventh day, respectively. These results strongly support the potential of developing FTIR microspectroscopy as a simple, reagent-free method for early detection of malignancy.
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Affiliation(s)
- Evgeny Bogomolny
- Ben Gurion University, Department of Physics, Beer-Sheva 84105, Israel
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39
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Petibois C, Déléris G. Chemical mapping of tumor progression by FT-IR imaging: towards molecular histopathology. Trends Biotechnol 2006; 24:455-62. [PMID: 16935373 DOI: 10.1016/j.tibtech.2006.08.005] [Citation(s) in RCA: 213] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2006] [Revised: 07/12/2006] [Accepted: 08/15/2006] [Indexed: 11/28/2022]
Abstract
Fourier-transform infrared (FT-IR) spectro-imaging enables global analysis of samples, with resolution close to the cellular level. Recent studies have shown that FT-IR imaging enables determination of the biodistribution of several molecules of interest (carbohydrates, lipids, proteins) for tissue analysis without pre-analytical modification of the sample such as staining. Molecular structure information is also available from the same analysis, notably for protein secondary structure and fatty acyl chain peroxidation level. Thus, several cancer markers can be identified from FT-IR tissue images, enabling accurate discrimination between healthy and tumor areas. FT-IR imaging applications are now able to provide unique chemical and morphological information about tissue status. With the fast image acquisition provided by modern mid-infrared imaging systems, it is now envisaged to analyze cerebral tumor exereses in delays compatible with neurosurgery. Accordingly, we propose to take FT-IR imaging into consideration for the development of new molecular histopathology tools.
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Affiliation(s)
- Cyril Petibois
- Université Victor Segalen Bordeaux 2, CNRS UMR 5084, CNAB, Bio-Organic Chemistry Group, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France.
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40
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Sahu RK, Argov S, Salman A, Zelig U, Huleihel M, Grossman N, Gopas J, Kapelushnik J, Mordechai S. Can Fourier transform infrared spectroscopy at higher wavenumbers (mid IR) shed light on biomarkers for carcinogenesis in tissues? JOURNAL OF BIOMEDICAL OPTICS 2005; 10:054017. [PMID: 16292977 DOI: 10.1117/1.2080368] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Fourier transform infrared microspectroscopy (FTIR-MSP) has shown promise as a technique for detection of abnormal cell proliferation and premalignant conditions. In the present study, we investigate the absorbance in the sensitive wavenumber region between 2800 and 3000 cm(-1), which has been known to be due to the antisymmetric and symmetric stretching vibrations of CH2 and CH3 groups of proteins and lipids. We report common biomarkers from this region that distinguish between normal and malignant tissues and cell lines. Based on our findings, we propose that the wavenumber region around 2800 to 3000 cm(-1) in the FTIR spectra of cells and tissues could provide valuable scientific evidence at the onset of premalignancy and may be used for ex vivo and in vitro detection of carcinogenesis. To further examine the utility of these markers in cancer diagnosis and management, they are tested successfully in monitoring the changes occurring in leukemia patients during chemotherapy.
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Affiliation(s)
- R K Sahu
- Ben Gurion University, Department of Physics and Cancer Research Center, Beer Sheva, Israel 84105
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41
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Mourant JR, Short KW, Carpenter S, Kunapareddy N, Coburn L, Powers TM, Freyer JP. Biochemical differences in tumorigenic and nontumorigenic cells measured by Raman and infrared spectroscopy. JOURNAL OF BIOMEDICAL OPTICS 2005; 10:031106. [PMID: 16229631 DOI: 10.1117/1.1928050] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Both infrared and Raman spectroscopies have the potential to noninvasively estimate the biochemical composition of mammalian cells, although this cannot be unambiguously determined from analysis approaches such as peak assignment or multivariate classification methods. We have developed a fitting routine that determines biochemical composition using basis spectra for the major types of biochemicals found in mammalian cells (protein, DNA, RNA, lipid and glycogen), which is shown to be robust and reproducible. We measured both infrared and Raman spectra of viable suspensions of pairs of nontumorigenic and tumorigenic rat fibroblast cell lines. To model in vivo conditions, we compared nonproliferating, nontumorigenic cells to proliferating, tumorigenic cells. Reproducible differences in biochemical composition were found for both nontumorigenic/tumorigenic cell models, using both spectroscopic techniques. These included an increased fraction of protein and nucleic acids in the tumorigenic cells, with a corresponding decrease in lipid and glycogen fractions. Measurements of each cell type in both the proliferating and nonproliferating states showed that proliferative status was the major determinant of differences in vibrational spectra, rather than tumorigenicity per se. The smallness of the spectral changes associated with tumorgenicity may be due to the subtle nature of the oncogenic change in this system (a single mutant oncogene).
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Affiliation(s)
- Judith R Mourant
- Los Alamos National Laboratory, MS E535, Bioscience Division, Los Alamos, New Mexico 87544, USA.
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42
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Abstract
The post-genomics era has brought with it ever increasing demands to observe and characterise variation within biological systems. This variation has been studied at the genomic (gene function), proteomic (protein regulation) and the metabolomic (small molecular weight metabolite) levels. Whilst genomics and proteomics are generally studied using microarrays (genomics) and 2D-gels or mass spectrometry (proteomics), the technique of choice is less obvious in the area of metabolomics. Much work has been published employing mass spectrometry, NMR spectroscopy and vibrational spectroscopic techniques, amongst others, for the study of variations within the metabolome in many animal, plant and microbial systems. This review discusses the advantages and disadvantages of each technique, putting the current status of the field of metabolomics in context, and providing examples of applications for each technique employed.
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Affiliation(s)
- Warwick B Dunn
- Bioanalytical Sciences Group, School of Chemistry, University of Manchester, Faraday Building, Sackville Street, P. O. Box 88, Manchester, UKM60 1QD.
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Sahu RK, Argov S, Salman A, Huleihel M, Grossman N, Hammody Z, Kapelushnik J, Mordechai S. Characteristic absorbance of nucleic acids in the Mid-IR region as possible common biomarkers for diagnosis of malignancy. Technol Cancer Res Treat 2005; 3:629-38. [PMID: 15560721 DOI: 10.1177/153303460400300613] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
FTIR spectroscopy has been extensively used to understand the differences between normal and malignant cells and tissues. In the present study, FTIR microspectroscopy was performed on biopsies to evaluate parameters deduced from changes in nucleic acid absorbance monitored at various characteristic wavenumbers in the Mid-IR region. The data showed that there were differences in the spectra of normal and malignant tissues from several organs such as colon, cervix, skin and blood with respect to absorbance due to nucleic acids. Similar results were observed in the case of cell lines that were transformed to induce carcinogenesis. Of the several ratios examined for consistency in differentiating cancer and normal tissues, the I(996 cm(-1))/I(966 cm(-1)) showed promise as a distinguishing parameter and was comparable to the I(1121 cm(-1))/I(1020 cm(-1)) ratio reported in many earlier studies. The absorbance of nucleic acids is presented with an emphasis on the application of FTIR microspectroscopy for diagnosis of malignancy. Our results indicate that usage of nucleic acid absorbance yield statistically significant parameters, which could differentiate normal and cancerous tissues.
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Affiliation(s)
- R K Sahu
- Dept. of Physics and the Cancer Research Center, Ben Gurion University, Beer-Sheva, 84105, Israel
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44
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Li QB, Xu Z, Zhang NW, Zhang L, Wang F, Yang LM, Wang JS, Zhou S, Zhang YF, Zhou XS, Shi JS, Wu JG. In vivo and in situ detection of colorectal cancer using Fourier transform infrared spectroscopy. World J Gastroenterol 2005; 11:327-30. [PMID: 15637737 PMCID: PMC4205330 DOI: 10.3748/wjg.v11.i3.327] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: Real-time and rapid identification of the malignant tissue can be performed during or before surgical operation. Here we aimed to detect in vivo and in situ colorectal cancer by using Fourier transform infrared (FTIR) spectroscopy and fiber-optic technology.
METHODS: A total of five patients with large intestine cancer were detected in vivo and in situ. Of them, three cases of colon cancer and one case of cecum cancer were detected intraoperatively and in vivo by using a FTIR spectrometer during surgical operation, and one case of rectum cancer was explored non-invasively and in vivo before the surgical operation. Normal and malignant colorectal tissues were detected in vivo and in situ using FTIR spectroscopy on the basis of fundamental studies.
RESULTS: There were significant differences between FTIR spectra of normal and malignant colorectal tissues detected in vivo and in situ. Experimental results revealed that the spectral characteristics of normal and malignant tissues found in vivo and in situ were similar to those obtained from in vitro measurement in our previous fundamental research.
CONCLUSION: FTIR fiber-optic attenuated total reflectance (ATR) spectroscopy can identify in situ and in vivo colorectal cancer. FTIR spectroscopic method with fiber optics is a non-invasive, rapid, accurate and in vivo cancer detection technique in clinical diagnosis.
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Affiliation(s)
- Qing-Bo Li
- The State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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Li QB, Sun XJ, Xu YZ, Yang LM, Zhang YF, Weng SF, Shi JS, Wu JG. Diagnosis of gastric inflammation and malignancy in endoscopic biopsies based on Fourier transform infrared spectroscopy. Clin Chem 2005; 51:346-50. [PMID: 15637129 DOI: 10.1373/clinchem.2004.037986] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Fourier transform infrared (FT-IR) spectroscopy is an effective tool for investigation of chemical changes at the molecular level. We previously demonstrated that FT-IR spectroscopy can reliably distinguish multiple types of carcinoma from healthy tissue. Because various stomach diseases are common, it is important to explore a noninvasive and rapid method to detect malignancy and gastritis in endoscopic biopsies. Our aim was to classify endoscopic biopsies into healthy, gastritis, and malignancy through the use of FT-IR spectroscopy. METHODS A total of 103 endoscopic samples, including 19 cases of cancer, 35 cases of chronic atrophic gastritis, 29 cases of chronic superficial gastritis, and 20 healthy tissue samples, were obtained at the First Hospital of Xi'an Jiaotong University, China. A modified attenuated total reflectance accessory was linked to a WQD-500 FT-IR spectrometer for biopsy measurement. The spectral characteristics for different types of tissues were correlated with the corresponding pathology results. The gastric biopsies were classified by FT-IR spectroscopy and a discriminant analysis method. RESULTS There were significant differences in the FT-IR spectra of four types of gastric biopsies. The discriminant analysis results demonstrated that the sensitivity of FT-IR detection for healthy, superficial gastritis, atrophic gastritis, and gastric cancer was 90%, 90%, 66%, 74%, respectively, which could help satisfy clinical diagnostic requirements. CONCLUSION FT-IR spectroscopy can distinguish disease processes in gastric endoscopic biopsies.
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Affiliation(s)
- Qing-Bo Li
- The State Key Laboratory of Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing, Peoples Republic of China
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Erukhimovitch V, Mukmanov I, Talyshinsky M, Souprun Y, Huleihel M. The use of FTIR microscopy for evaluation of herpes viruses infection development kinetics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2004; 60:2355-2361. [PMID: 15249025 DOI: 10.1016/j.saa.2003.12.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2003] [Accepted: 12/05/2003] [Indexed: 05/24/2023]
Abstract
The kinetics of Herpes simplex infection development was studied using an FTIR microscopy (FTIR-M) method. The family of herpes viruses includes several members like H. simplex types I and II (HSV I, II), Varicella zoster (VZV) viruses which are involved in various human and animal infections of different parts of the body. In our previous study, we found significant spectral differences between normal uninfected cells in cultures and cells infected with herpes viruses at early stages of the infection. In the present study, cells in cultures were infected with either HSV-I or VZV and at various times post-infection they were examined either by optical microscopy or by advanced FTIR-M. Spectroscopic measurements show a consistent decrease in the intensity of the carbohydrate peak in correlation with the viral infection development, observed by optical microscopy. This decrease in cellular carbohydrate level was used as indicator for herpes viruses infection kinetics. This parameter could be used as a basis for applying a spectroscopic method for the evaluation of herpes virus infection development. Our results show also that the development kinetics of viral infection has an exponential character for these viruses.
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Affiliation(s)
- Vitaly Erukhimovitch
- The Institute for Applied Biosciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Arakawa ET, Lavrik NV, Rajic S, Datskos PG. Detection and differentiation of biological species using microcalorimetric spectroscopy. Ultramicroscopy 2003; 97:459-65. [PMID: 12801702 DOI: 10.1016/s0304-3991(03)00074-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We report on the application of infrared (IR) microcalorimetric spectroscopy ( micro -CalSpec) to the identification and detection of trace amounts of biological species. Our approach combines principles of photothermal IR spectroscopy with ultrasensitive microcantilever (MC) thermal detectors. We have obtained photothermal IR spectra for DNA and RNA bases and for Bacillus Cereus (an anthrax simulant) in the wavelength range of 2.5-14.5 micro m (4000-690 cm(-1)). The measurements are accomplished by absorbing biological materials directly on a MC thermal detector. The main advantage of the developed micro -CalSpec is its unprecedented sensitivity as compared to any of the previously explored IR techniques, including FTIR and photothermal FTIR methods. Our results demonstrate that <10(-9)g of a biological sample is sufficient to obtain its characteristic micro -CalSpec spectrum that contains information-rich chemical (vibrational) signatures. This opens up a new opportunity to create inexpensive high-throughput analytical systems for biochemical detection.
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Affiliation(s)
- E T Arakawa
- Oak Ridge National Laboratory, 1 Bear Creek Rd. Oak Ridge, TN 37831-8039, USA
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Huleihel M, Talyshinsky M, Souprun Y, Erukhimovitch V. Spectroscopic evaluation of the effect of a red microalgal polysaccharide on herpes-infected Vero cells. APPLIED SPECTROSCOPY 2003; 57:390-395. [PMID: 14658634 DOI: 10.1366/00037020360625916] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The sulfated polysaccharide obtained from a species of red microalga has proved to be a potent antiviral agent against various members of the herpes family. In the present study, we used microscopic Fourier transform infrared spectroscopy (FT-IR) to investigate differences between normal cells, those infected with herpes viruses, and infected cells treated with red microalgal polysaccharide. FT-IR enables the characterization of cell or tissue pathology based on characteristic molecular vibrational spectra of the cells. The advantage of microscopic FT-IR spectroscopy over conventional FT-IR spectroscopy is that it facilitates inspection of restricted regions of cell cultures or tissue. Our results showed significant spectral differences at early stages of infection between infected and noninfected cells, and between infected cells treated with the polysaccharide and those not treated. In infected cells, there was an impressive decrease in sugar content and a considerable increase in phosphate levels in conjunction with the infection progress. Our results also proved that sugars penetrated and accumulated inside cells treated with the red microalgal polysaccharide. These could have been sugar fragments of low molecular weight present in the polysaccharide solution, despite purification by dialysis. Such sugar accumulation might be responsible for a breakdown in the internal steps of the viral replication cycle.
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Affiliation(s)
- Mahmoud Huleihel
- The Institute for Applied Biosciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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49
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Salman A, Ramesh J, Erukhimovitch V, Talyshinsky M, Mordechai S, Huleihel M. FTIR microspectroscopy of malignant fibroblasts transformed by mouse sarcoma virus. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 2003; 55:141-53. [PMID: 12628697 DOI: 10.1016/s0165-022x(02)00182-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Fourier transform infrared microspectroscopy (FTIR-MSP), which is based on the characteristic molecular vibrational spectra of cells, was used to investigate spectral differences between normal primary rabbit bone marrow (BM) cells and bone marrow cells transformed (BMT) by murine sarcoma virus (MuSV). Primary cells, rather than cell lines, were used for this research because primary cells are similar to normal tissue cells in most of their characteristics. Our results showed dramatic changes in absorbance between the control cells and MuSV124-transformed cells. Various biological markers, such as the phosphate level and the RNA/DNA obtained, based on the analysis of the FTIR-MSP spectra, also displayed significant differences between the control and transformed cells. Preliminary results suggested that the cluster analysis performed on the FTIR-MSP spectra yielded 100% accuracy in classifying both types of cells.
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MESH Headings
- Amides/analysis
- Amides/chemistry
- Amides/metabolism
- Animals
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/chemistry
- Biomarkers, Tumor/metabolism
- Bone Marrow Cells/chemistry
- Bone Marrow Cells/classification
- Bone Marrow Cells/metabolism
- Bone Marrow Cells/virology
- Cell Transformation, Viral
- Cluster Analysis
- DNA, Neoplasm/analysis
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/metabolism
- Fibroblasts/chemistry
- Fibroblasts/classification
- Fibroblasts/metabolism
- Fibroblasts/pathology
- Fibroblasts/virology
- Mice
- Microspectrophotometry/methods
- Phosphates/analysis
- Phosphates/chemistry
- Phosphates/metabolism
- RNA, Neoplasm/analysis
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/metabolism
- Rabbits
- Reference Values
- Sarcoma Viruses, Murine
- Spectroscopy, Fourier Transform Infrared/methods
- Tumor Cells, Cultured
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Affiliation(s)
- Ahmad Salman
- Department of Physics, Ben Gurion University of the Negev, 84105, Beer-Sheva, Israel
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50
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Erukhimovitch V, Talyshinsky M, Souprun Y, Huleihel M. Spectroscopic characterization of human and mouse primary cells, cell lines and malignant cells. Photochem Photobiol 2002; 76:446-51. [PMID: 12405154 DOI: 10.1562/0031-8655(2002)076<0446:scoham>2.0.co;2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fourier transform infrared (FTIR) spectroscopy is currently being developed as a new optical approach to the diagnosis and characterization of cell or tissue pathology. The advantage of FTIR microspectroscopy over conventional FTIR spectroscopy in the diagnosis of malignancies is that it facilitates inspection of restricted regions of the cell culture or tissue. In this study, we set out to evaluate FTIR microspectroscopy as a diagnostic tool for identifying retrovirus-induced malignancies. Our study showed significant and consistent differences between cultures of different types of cells of both mouse and human origin, i.e. primary fibroblast cells (one to two passages in cell culture), fibroblast cell lines and malignant cells transformed by murine sarcoma virus. An impressive decrease in the levels of phosphate and other metabolites was seen in malignant cells compared with primary cells. The levels of these metabolites in the cell lines were significantly lower than in the primary cells but higher than in the malignant cells. In addition, the peak attributed to the PO2- symmetric stretching mode at 1082 cm(-1) in primary cells shifted significantly to 1085 cm(-1) for the cell line and to 1087 cm(-1) for the malignant cells. These differences taken together with differences in the shapes of various bands throughout the spectrum strongly support the possibility of developing FTIR microspectroscopy for the detection and study of malignant--and possibly premalignant--cells.
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Affiliation(s)
- Vitaly Erukhimovitch
- The Institute for Applied Biosciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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