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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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2
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Bratash O, Buhot A, Leroy L, Engel E. Optical fiber biosensors toward in vivo detection. Biosens Bioelectron 2024; 251:116088. [PMID: 38335876 DOI: 10.1016/j.bios.2024.116088] [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: 12/19/2023] [Revised: 01/19/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024]
Abstract
This review takes stock of the various optical fiber-based biosensors that could be used for in vivo applications. We discuss the characteristics that biosensors must have to be suitable for such applications and the corresponding transduction modes. In particular, we focus on optical fiber biosensors based on fluorescence, evanescent wave, plasmonics, interferometry, and Raman phenomenon. The operational principles, implemented solutions, and performances are described and debated. The different sensing configurations, such as the side- and tip-based fiber biosensors, are illustrated, and their adaptation for in vivo measurements is discussed. The required implementation of multiplexed biosensing on optical fibers is shown. In particular, the use of multi-fiber assemblies, one of the most optimal configurations for multiplexed detection, is discussed. Different possibilities for multiple localized functionalizations on optical fibers are presented. A final section is devoted to the practical in vivo use of fiber-based biosensors, covering regulatory, sterilization, and packaging aspects. Finally, the trends and required improvements in this promising and emerging field are analyzed and discussed.
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Affiliation(s)
- Oleksii Bratash
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000, Grenoble, France
| | - Arnaud Buhot
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000, Grenoble, France
| | - Loïc Leroy
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000, Grenoble, France
| | - Elodie Engel
- Univ. Grenoble Alpes, CEA, CNRS, Grenoble INP, IRIG, SyMMES, 38000, Grenoble, France.
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3
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Wetzel C, Jansen-Olliges L, Stadler M, Surup F, Zeilinger C, Roth B. Analysis of SARS-CoV-2 spike RBD binding to ACE2 and its inhibition by fungal cohaerin C using surface enhanced Raman spectroscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4097-4111. [PMID: 37799683 PMCID: PMC10549735 DOI: 10.1364/boe.495685] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/26/2023] [Indexed: 10/07/2023]
Abstract
The structure of the SARS-CoV-2 spike RBD and human ACE2 as well as changes in the structure due to binding activities were analysed using surface enhanced Raman spectroscopy. The inhibitor cohaerin C was applied to inhibit the binding between spike RBD and ACE2. Differences and changes in the Raman spectra were determined using deconvolution of the amide bands and principal component analysis. We thus demonstrate a fast and label-free analysis of the protein structures and the differentiation between bound and unbound states. The approach is suitable for sensing and screening and might be relevant to investigate other protein systems as well.
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Affiliation(s)
- Christoph Wetzel
- Leibniz University Hannover, Hannover Centre for Optical Technologies, Nienburger Str. 17, 30167 Hannover, Germany
| | - Linda Jansen-Olliges
- Leibniz University Hannover, Centre of Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Marc Stadler
- Helmholtz Centre for Infection Research GmbH, Department Microbial Drugs, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Frank Surup
- Helmholtz Centre for Infection Research GmbH, Department Microbial Drugs, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Technische Universität Braunschweig, Institute of Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Carsten Zeilinger
- Leibniz University Hannover, Centre of Biomolecular Drug Research, Schneiderberg 38, 30167 Hannover, Germany
| | - Bernhard Roth
- Leibniz University Hannover, Hannover Centre for Optical Technologies, Nienburger Str. 17, 30167 Hannover, Germany
- Leibniz University Hannover, Cluster of Excellence PhoenixD, Welfenplatz 1, 30167 Hannover, Germany
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4
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Durinova E, Mojzes P, Bily T, Franta Z, Fessl T, Borodavka A, Tuma R. Shedding light on reovirus assembly-Multimodal imaging of viral factories. Adv Virus Res 2023; 116:173-213. [PMID: 37524481 DOI: 10.1016/bs.aivir.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Avian (ortho)reovirus (ARV), which belongs to Reoviridae family, is a major domestic fowl pathogen and is the causative agent of viral tenosynovitis and chronic respiratory disease in chicken. ARV replicates within cytoplasmic inclusions, so-called viral factories, that form by phase separation and thus belong to a wider class of biological condensates. Here, we evaluate different optical imaging methods that have been developed or adapted to follow formation, fluidity and composition of viral factories and compare them with the complementary structural information obtained by well-established transmission electron microscopy and electron tomography. The molecular and cellular biology aspects for setting up and following virus infection in cells by imaging are described first. We then demonstrate that a wide-field version of fluorescence recovery after photobleaching is an effective tool to measure fluidity of mobile viral factories. A new technique, holotomographic phase microscopy, is then used for imaging of viral factory formation in live cells in three dimensions. Confocal Raman microscopy of infected cells provides "chemical" contrast for label-free segmentation of images and addresses important questions about biomolecular concentrations within viral factories and other biological condensates. Optical imaging is complemented by electron microscopy and tomography which supply higher resolution structural detail, including visualization of individual virions within the three-dimensional cellular context.
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Affiliation(s)
- Eva Durinova
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Peter Mojzes
- Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Tomas Bily
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic; Biology Centre, Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | - Zdenek Franta
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Tomas Fessl
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Roman Tuma
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic.
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5
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Lin C, Li Y, Peng Y, Zhao S, Xu M, Zhang L, Huang Z, Shi J, Yang Y. Recent development of surface-enhanced Raman scattering for biosensing. J Nanobiotechnology 2023; 21:149. [PMID: 37149605 PMCID: PMC10163864 DOI: 10.1186/s12951-023-01890-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 04/10/2023] [Indexed: 05/08/2023] Open
Abstract
Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.
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Affiliation(s)
- Chenglong Lin
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yanyan Li
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yusi Peng
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Shuai Zhao
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Meimei Xu
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Graduate School of the Chinese Academy of Sciences, No.19(A) Yuquan Road, Beijing, 100049, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Lingxia Zhang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhengren Huang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Jianlin Shi
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Yong Yang
- State Key Laboratory of High-Performance Ceramics and Superfine Microstructures, Shanghai Institute of Ceramics, Chinese Academy of Sciences, 1295 Dingxi Road, Shanghai, 200050, People's Republic of China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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Targeting erythrocyte-mediated hypoxia to alleviate lung injury induced by pyrrolizidine alkaloids. Arch Toxicol 2023; 97:819-829. [PMID: 36639515 DOI: 10.1007/s00204-023-03443-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are widely distributed natural toxins and have been extensively studied for their hepatotoxicity. However, PA-induced pulmonary toxicity remains less studied regarding the initiating mechanism and treatment approaches. Our previous study demonstrated the formation of pyrrole-hemoglobin adducts after PA exposure in vivo, which is suspected to affect the oxygen-carrying capacity of erythrocytes [red blood cells (RBCs)] consequently. The present study aimed to investigate the effects of PAs on the oxygen-carrying capacity of RBCs and the potential of targeting RBC-mediated hypoxia to alleviate PA-induced lung injury. First, rats were treated with retrorsine (RTS) or monocrotaline (MCT) intravenously at 0.2 mmol/kg. The results of Raman spectrometry analysis on blood samples revealed both RTS and MCT significantly reduced the oxygen-carrying capacity of RBCs. Further, MCT (0.2 mmol/kg) was orally given to the rats with or without pretreatment with two doses of erythropoietin (Epo, 500 IU/kg/dose every other day), an RBC-stimulating agent. Biochemical and histological results showed pretreatment with Epo effectively reduced the cardiopulmonary toxicity induced by MCT. These findings provide the first evidence that adduction on hemoglobin, and the resulting RBC damage and impaired oxygen-carrying capacity, are the major initiating mechanism underlying PA-induced pulmonary arterial hypertension (PAH), while targeting the RBC damage is a potential therapeutic approach for PA-induced lung injury.
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Zebrafish Models to Study Ectopic Calcification and Calcium-Associated Pathologies. Int J Mol Sci 2023; 24:ijms24043366. [PMID: 36834795 PMCID: PMC9967340 DOI: 10.3390/ijms24043366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/20/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Ectopic calcification refers to the pathological accumulation of calcium ions in soft tissues and is often the result of a dysregulated action or disrupted function of proteins involved in extracellular matrix mineralization. While the mouse has traditionally been the go-to model organism for the study of pathologies associated with abnormal calcium deposition, many mouse mutants often have exacerbated phenotypes and die prematurely, limiting the understanding of the disease and the development of effective therapies. Since the mechanisms underlying ectopic calcification share some analogy with those of bone formation, the zebrafish (Danio rerio)-a well-established model for studying osteogenesis and mineralogenesis-has recently gained momentum as a model to study ectopic calcification disorders. In this review, we outline the mechanisms of ectopic mineralization in zebrafish, provide insights into zebrafish mutants that share phenotypic similarities with human pathological mineralization disorders, list the compounds capable of rescuing mutant phenotypes, and describe current methods to induce and characterize ectopic calcification in zebrafish.
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8
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Watanabe TM, Sasaki K, Fujita H. Recent Advances in Raman Spectral Imaging in Cell Diagnosis and Gene Expression Prediction. Genes (Basel) 2022; 13:2127. [PMID: 36421802 PMCID: PMC9690875 DOI: 10.3390/genes13112127] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 06/30/2024] Open
Abstract
Normal and tumor regions within cancer tissue can be distinguished using various methods, such as histological analysis, tumor marker testing, X-ray imaging, or magnetic resonance imaging. Recently, new discrimination methods utilizing the Raman spectra of tissues have been developed and put into practical use. Because Raman spectral microscopy is a non-destructive and non-labeling method, it is potentially compatible for use in the operating room. In this review, we focus on the basics of Raman spectroscopy and Raman imaging in live cells and cell type discrimination, as these form the bases for current Raman scattering-based cancer diagnosis. We also review recent attempts to estimate the gene expression profile from the Raman spectrum of living cells using simple machine learning. Considering recent advances in machine learning techniques, we speculate that cancer type discrimination using Raman spectroscopy will be possible in the near future.
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Affiliation(s)
- Tomonobu M. Watanabe
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Minami-ku, Hiroshima 734-8553, Japan
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Kobe 650-0047, Japan
| | - Kensuke Sasaki
- Laboratory for Comprehensive Bioimaging, RIKEN Center for Biosystems Dynamics Research (BDR), 2-2-3 Minatojima-minamimachi, Kobe 650-0047, Japan
| | - Hideaki Fujita
- Department of Stem Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, 1-2-3 Minami-ku, Hiroshima 734-8553, Japan
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Roa-Velázquez D, Xoconostle-Cázares B, Benítez-Cardoza CG, Ortega-López J, Shoshani L, Morales-Ríos E, Gallardo-Hernández S. Expression, purification, and refolding of the recombinant extracellular domain β 1-subunit of the dog Na +/K +-ATPase of the epithelial cells. Protein Expr Purif 2022; 200:106167. [PMID: 36057422 DOI: 10.1016/j.pep.2022.106167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/25/2022]
Abstract
The β1-subunit of the Na+/K+-ATPase is a cell membrane protein, beyond its classic functions, it is also a cell adhesion molecule. β1-subunits on the lateral membrane of dog kidney epithelial cells trans-interact with β1-subunits from another neighboring cells. The β-β interaction is essential for the formation and stabilization of intercellular junctions. Previous studies on site-directed mutagenesis and in silico revealed that the interaction interface involves residues 198-207 and 221-229. However, it is necessary to report the interaction interface at the structural level experimentally. Here, we describe the successful cloning, overexpression in E. coli, and purification of the extracellular domain of the β1-subunit from inclusion bodies. Experimental characterization by size exclusion chromatography and DLS indicated similar hydrodynamic properties of the protein refolded. Structural analysis by circular dichroism and Raman spectroscopy revealed the secondary structures in the folded protein of type β-sheet, α-helix, random coil, and turn. We also performed β1-β1 interaction assays with the recombinant protein, showing dimers' formation (6xHisβ1-β1). Given our results, the recombinant extracellular domain of the β1-subunit is highly similar to the native protein, therefore the current work in our laboratory aims to characterize at the atomic level the interaction interface between EDβ1.
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Affiliation(s)
- Daniela Roa-Velázquez
- Programa de Doctorado en Nanociencias y Nanotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Beatriz Xoconostle-Cázares
- Departamento de Bioingeniería y Biotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica, Escuela Nacional de Medicina y Homeopatía-Instituto Politécnico Nacional, Guillermo Massieu Helguera 239, Ciudad de México, 07320, Mexico.
| | - Jaime Ortega-López
- Departamento de Bioingeniería y Biotecnología, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Liora Shoshani
- Departamento de Fisiología Biofísica y Neurociencias, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Edgar Morales-Ríos
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
| | - Salvador Gallardo-Hernández
- Departamento de Física, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Av. IPN 2508, Ciudad de México, 07360, Mexico.
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Effect of pH and protein-polysaccharide ratio on the intermolecular interactions between amaranth proteins and xanthan gum to produce electrostatic hydrogels. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107648] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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Eskandari V, Sahbafar H, Zeinalizad L, Hadi A. A review of applications of surface-enhanced raman spectroscopy laser for detection of biomaterials and a quick glance into its advances for COVID-19 investigations. ISSS JOURNAL OF MICRO AND SMART SYSTEMS 2022; 11:363-382. [PMID: 35540110 PMCID: PMC9070975 DOI: 10.1007/s41683-022-00103-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/19/2022] [Accepted: 03/27/2022] [Indexed: 11/28/2022]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is one of the most sensitive analytical tools. In some cases, it is possible to record a high-quality SERS spectrum in which even a single molecule is involved. Therefore, SERS is considered a significantly promising option as an alternative to routine analytical techniques used in food, environmental, biochemical, and medical analyzes. In this review, the definitive applications of SERS developed to identify biochemically important species (especially medical and biological) from the simplest to the most complex are briefly discussed. Moreover, the potential capability of SERS for being used as an alternative to routine methods in diagnostic and clinical cases is demonstrated. In addition, this article describes how SERS-based sensors work, addresses its advancements in the last 20 years, discusses its applications for detecting Coronavirus Disease 2019 (COVID-19), and finally describes future works. The authors hope that this article will be useful for researchers who want to enter this amazing field of research.
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Affiliation(s)
- Vahid Eskandari
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Hossein Sahbafar
- School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Leila Zeinalizad
- Faculty of Biomedical Engineering, Department of Mechanical Engineering, Iran University of Science and Technology, Tehran, Iran
| | - Amin Hadi
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
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12
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Wang Z, Xue T, Zhang T, Wang X, Zhang H, Gao Z, Zhou Q, Gao E, Zhang T, Li Z. Identification of compositional and structural changes in the nucleus pulposus of patients with cervical disc herniation by Raman spectroscopy. Front Endocrinol (Lausanne) 2022; 13:1015198. [PMID: 36277712 PMCID: PMC9585164 DOI: 10.3389/fendo.2022.1015198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/20/2022] [Indexed: 11/19/2022] Open
Abstract
PURPOSE Cervical disc herniation (CDH) is one of the most common spinal diseases in modern society; intervertebral disc degeneration (IVDD) has long been considered as its primary cause. However, the mechanism of intervertebral disc degeneration is still unclear. The aim of the study is to examine the components and structures of proteoglycan and collagen in cervical disc herniated nucleus pulposus (NP) using a validated and convenient Raman spectra technique and histological methods to further elucidate the mechanism of IVDD at the microscopic level. METHODS Our study used a burgeoning technique of Raman spectroscopy combined with in vitro intervertebral disc NP to characterize the above mentioned research purposes. Firstly, we collected cervical disc NP samples and imaging data by certain inclusion and exclusion criteria. Then, we graded the NP of the responsible segment according to the patient's preoperative cervical magnetic resonance imaging (MRI) T2-weighted images by Pfirrmann grading criteria while measuring the T2 signal intensity value of NP. In addition, the structure of the NP samples was evaluated by histological staining (H&E staining and Safranin-O staining). Finally, the samples were scanned and analyzed by Raman spectroscopy. RESULTS A total of 28 NP tissues from 26 patients (two of these patients were cases that involved two segments) with CDH were included in this study. According to the Raman spectroscopy scan, the relative content of proteoglycans which is characterized by the ratio of the two peaks (I 1,064/ I 1,004) in the NP showed a significantly negative correlation with Pfirrmann grade (P < 0.001), while the collagen content and the NP intensity value showed a positive correlation (P < 0.001). For the microstructural characterization of collagen, we found that it may have an essential role in the degenerative process of the intervertebral disc. Moreover, histological staining (H&E staining and Safranin-O staining) showed the general structure of the NP and the distribution of macromolecules. CONCLUSION The present study demonstrated the possibility of characterizing the macromolecular substances inside the cervical disc NP tissue by Raman spectroscopy. It also confirmed that macromolecular substances such as proteoglycans and collagen have some degree of alteration in content and structure during degeneration, which has a further positive significance for the elucidation of CDH's mechanism.
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Affiliation(s)
- Zhiqi Wang
- Department of Orthopedic, Tianjin First Central Hospital, Tianjin, China
| | - Tao Xue
- School of Materials Science and Engineering, Tianjin University, Tianjin, China
| | - Tongxing Zhang
- Department of Minimally Invasive Spine Surgery, Tianjin Hospital, Tianjin University, Tianjin, China
| | - Xuehui Wang
- Department of Orthopedic and Joint Sports Medicine, The First Affiliated Hospital of Baotou Medical College, Baotou, China
| | - Hui Zhang
- Department of Orthopedic, Tianjin First Central Hospital, Tianjin, China
| | - Zhongyu Gao
- Department of Orthopedic, Tianjin First Central Hospital, Tianjin, China
| | - Qiang Zhou
- Department of Orthopedic, Tianjin First Central Hospital, Tianjin, China
| | - Erke Gao
- First Central Clinical College, Tianjin Medical University, Tianjin, China
| | - Tao Zhang
- Department of Orthopedic, Tianjin First Central Hospital, Tianjin, China
- *Correspondence: Tao Zhang, ; Zhaoyang Li,
| | - Zhaoyang Li
- School of Materials Science and Engineering, Tianjin University, Tianjin, China
- *Correspondence: Tao Zhang, ; Zhaoyang Li,
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Kuhar N, Sil S, Umapathy S. Potential of Raman spectroscopic techniques to study proteins. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119712. [PMID: 33965670 DOI: 10.1016/j.saa.2021.119712] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/23/2021] [Accepted: 03/12/2021] [Indexed: 05/18/2023]
Abstract
Proteins are large, complex molecules responsible for various biological processes. However, protein misfolding may lead to various life-threatening diseases. Therefore, it is vital to understand the shape and structure of proteins. Despite numerous techniques, a mechanistic understanding of the protein folding process is still unclear. Therefore, new techniques are continually being explored. In the present article, we have discussed the importance of Raman spectroscopy, Raman Optical Activity (ROA) and various other advancements in Raman spectroscopy to understand protein structure and conformational changes based on the review of our earlier work and recent literature. A Raman spectrum of a protein provides unique signatures for various secondary structures like helices, beta-sheets, turns, random structures, etc., and various amino acid residues such as tyrosine, tryptophan, and phenylalanine. We have shown how Raman spectra can differentiate between bovine serum albumin (BSA) and lysozyme protein based on their difference in sequence and structure (primary, secondary and tertiary). Although it is challenging to elucidate the structure of a protein using a Raman spectrum alone, Raman spectra can be used to differentiate small changes in conformations of proteins such as BSA during melting. Various new advancements in technique and data analyses in Raman spectroscopic studies of proteins have been discussed. The last part of the review focuses on the importance of the ROA spectrum to understand additional features about proteins. The ROA spectrum is rich in information about the protein backbone due to its rigidity compared to its side chains. Furthermore, the ROA spectra of lysozyme and BSA have been presented to show how ROA provides extra information about the solvent properties of proteins.
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Affiliation(s)
- Nikki Kuhar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India
| | - Sanchita Sil
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India; Defence Bioengineering and Electromedical Laboratory (DEBEL), Defence Research and Development Organization (DRDO), C V Raman Nagar, Bangalore 560 093, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bengaluru 560 012, Karnataka, India; Department of Instrumentation & Applied Physics, Indian Institute of Science, Bengaluru 560 012, Karnataka, India.
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14
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Ghosh T, Mondal A, Vamsi Bharadwaj SV, Mishra S. A naturally fluorescent protein C-phycoerythrin and graphene oxide bio-composite as a selective fluorescence 'turn off/on' probe for DNA quantification and characterization. Int J Biol Macromol 2021; 185:644-653. [PMID: 34217741 DOI: 10.1016/j.ijbiomac.2021.06.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Highly specific graphene-DNA interactions have been at the forefront of graphene-based sensor design for various analytes, including DNA itself. However, in addition to its detection, DNA also needs to be characterized according to its size and concentration in a sample, which is an additional analytical step. Designing a highly sensitive and selective DNA sensing and characterization platform is, thus, of great interest. The present study demonstrates that a bio-derived, naturally fluorescent protein C-phycoerythrin (CPE) - graphene oxide (GO) bio-composite can be used to detect dsDNA in nanomolar quantities efficiently via fluorescent "turn off/on" mechanism. Interaction with GO temporarily quenches CPE fluorescence in a dose-dependent manner. Analytical characterization indicates an indirect charge transfer with a corresponding loss of crystalline GO structure. The fluorescence is regained with the addition of DNA, while other biomolecules do not pose any hinderance in the detection process. The extent of regain is DNA length dependent, and the corresponding calibration curve successfully quantifies the size of an unknown DNA. The incubation time for detection is ~3-5 min. The bio-composite platform also works successfully in a complex biomolecule matrix and cell lysate. However, the presence of serum albumin poses a hinderance in the serum sample. Particle size analysis proves that CPE displacement from GO surface by the incoming DNA is the reason for the 'turn on' response, and that the sensing process is exclusive to dsDNA. This new platform could be an exciting and rapid DNA sensing and characterization tool.
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Affiliation(s)
- Tonmoy Ghosh
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Aniruddha Mondal
- Inorganic Materials and Catalysis Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - S V Vamsi Bharadwaj
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
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15
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Lin D, Hsieh CL, Hsu KC, Liao PH, Qiu S, Gong T, Yong KT, Feng S, Kong KV. Geometrically encoded SERS nanobarcodes for the logical detection of nasopharyngeal carcinoma-related progression biomarkers. Nat Commun 2021; 12:3430. [PMID: 34078895 PMCID: PMC8173014 DOI: 10.1038/s41467-021-23789-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/12/2021] [Indexed: 02/08/2023] Open
Abstract
The limited availability of nasopharyngeal carcinoma-related progression biomarker array kits that offer physicians comprehensive information is disadvantageous for monitoring cancer progression. To develop a biomarker array kit, systematic identification and differentiation of a large number of distinct molecular surface-enhanced Raman scattering (SERS) reporters with high spectral temporal resolution is a major challenge. To address this unmet need, we use the chemistry of metal carbonyls to construct a series of unique SERS reporters with the potential to provide logical and highly multiplex information during testing. In this study, we report that geometric control over metal carbonyls on nanotags can produce 14 distinct barcodes that can be decoded unambiguously using commercial Raman spectroscopy. These metal carbonyl nanobarcodes are tested on human blood samples and show strong sensitivity (0.07 ng/mL limit of detection, average CV of 6.1% and >92% degree of recovery) and multiplexing capabilities for MMPs.
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Affiliation(s)
- Duo Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Chang-Lin Hsieh
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Keng-Chia Hsu
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Pei-Hsuan Liao
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Sufang Qiu
- Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, Fujian, China
| | - Tianxun Gong
- State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Electronic Science and Engineering (National Exemplary School of Microelectronics), University of Electronic Science and Technology of China, Chengdu, China
| | - Ken-Tye Yong
- School of Biomedical Engineering, The University of Sydney, Sydney, NSW, Australia
- The University of Sydney Nano Institute, The University of Sydney, Sydney, NSW, Australia
| | - Shangyuan Feng
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou, Fujian, China
| | - Kien Voon Kong
- Department of Chemistry, National Taiwan University, Taipei, Taiwan.
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16
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韦 仲, 毛 华, 黄 富, 钟 会, 黄 丽, 黎 远, 卢 敏, 金 少. [Application of fiber Raman endoscopic probe in the diagnosis of gastric cancer]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019; 39:1506-1510. [PMID: 31907156 PMCID: PMC6942980 DOI: 10.12122/j.issn.1673-4254.2019.12.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To develop a fiber Raman endoscopic probe that can be integrated in a gastroscope and evaluate its value in the diagnosis of gastric cancer. METHODS The Raman spectra of gastric cancer tissues and normal tissues were obtained using the fiber Raman endoscopic probe and confocal microRaman spectroscopy. After preprocessing with smoothing, baseline elimination and normalization, the spectroscopic data were analyzed by the principle component analyses combined with stechiometry. Based on the pathological results, the diagnostic accuracy, sensitiveness and specificity of Raman spectroscopy combined with stechiometry were evaluated. RESULTS The fiber Raman endoscopic probe and microRaman spectroscopy revealed significantly different Raman spectra between gastric cancer tissues and normal tissues. The diagnostic accuracy, sensitiveness and specificity of the fiber Raman endoscopic probe was 80.56%, 88.89%, and 84.72% for gastric cancer, respectively. CONCLUSIONS The fiber Raman endoscopic probe combined with stechiometry provides an effective modality for the diagnosis of gastric cancer and can well distinguish gastric cancer tissue from normal gastric tissues.
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Affiliation(s)
- 仲 韦
- 南方医科大学珠江医院,广东 广州 510282Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 华 毛
- 南方医科大学珠江医院,广东 广州 510282Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 富荣 黄
- 暨南大学光电工程系,广东 广州 510632Department of Photoelectric Engineering, Jinan University, Guangzhou 510632, China
| | - 会清 钟
- 华南师范大学生物光子学研究院,广东 广州 510631Institute of Biological Photonics, South China Normal University, Guangzhou 510631, China
| | - 丽韫 黄
- 南方医科大学珠江医院,广东 广州 510282Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 远鹏 黎
- 暨南大学光电工程系,广东 广州 510632Department of Photoelectric Engineering, Jinan University, Guangzhou 510632, China
| | - 敏 卢
- 南方医科大学珠江医院,广东 广州 510282Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - 少琴 金
- 南方医科大学珠江医院,广东 广州 510282Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
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17
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Kniggendorf AK, Schmidt D, Roth B, Plettenburg O, Zeilinger C. pH-Dependent Conformational Changes of KcsA Tetramer and Monomer Probed by Raman Spectroscopy. Int J Mol Sci 2019; 20:ijms20112736. [PMID: 31167355 PMCID: PMC6601014 DOI: 10.3390/ijms20112736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 05/24/2019] [Accepted: 06/02/2019] [Indexed: 11/30/2022] Open
Abstract
KcsA is a tetrameric potassium channel formed out of four identical monomeric subunits used as a standard model for selective potassium transport and pH-dependent gating. Large conformational changes are reported for tetramer and monomer upon gating, and the response of the monomer being controversial with the two major studies partially contradicting each other. KcsA was analyzed as functional tetramers embedded in liposomes and as monomer subunits with confocal Raman microscopy under physiological conditions for the active and the closed channel state, using 532 nm excitation to avoid introducing conformational changes during the measurement. Channel function was confirmed using liposome flux assay. While the classic fingerprint region below 1800 rel. cm−1 in the Raman spectrum of the tetramer was unaffected, the CH-stretching region between 2800 and 3200 rel. cm−1 was found to be strongly affected by the conformation. No pH-dependency was observed in the Raman spectra of the monomer subunits, which closely resembled the Raman spectrum of the tetramer in its active conformation, indicating that the open conformation of the monomer and not the closed conformation as postulated may equal the relaxed state of the molecule.
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Affiliation(s)
- Ann-Kathrin Kniggendorf
- Gottfried Wilhelm Leibniz Universität Hannover, Hannover Centre for Optical Technologies (HOT), Nienburger Straße 17, 30167 Hannover, Germany.
| | - David Schmidt
- Gottfried Wilhelm Leibniz Universität Hannover, Naturwissenschaftliche Fakultät, Center of Biomolecular Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Bernhard Roth
- Gottfried Wilhelm Leibniz Universität Hannover, Hannover Centre for Optical Technologies (HOT), Nienburger Straße 17, 30167 Hannover, Germany.
- Cluster of Excellence PhoenixD, Leibniz University Hannover, Welfengarten 1, 30167 Hannover, Germany.
| | - Oliver Plettenburg
- Gottfried Wilhelm Leibniz Universität Hannover, Naturwissenschaftliche Fakultät, Center of Biomolecular Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
- Institute of Medicinal Chemistry, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
| | - Carsten Zeilinger
- Gottfried Wilhelm Leibniz Universität Hannover, Naturwissenschaftliche Fakultät, Center of Biomolecular Research (BMWZ), Schneiderberg 38, 30167 Hannover, Germany.
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18
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de la O-Cuevas E, Badillo-Ramírez I, Islas SR, Araujo-Andrade C, Saniger JM. Sensitive Raman detection of human recombinant interleukin-6 mediated by DCDR/GERS hybrid platforms. RSC Adv 2019; 9:12269-12275. [PMID: 35515877 PMCID: PMC9063685 DOI: 10.1039/c9ra01396b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
Recombinant human interleukin-6 (IL-6) is a key cytokine that plays an important role in the immune system and inflammatory response, explaining why any modification of its concentration in biological fluids is considered a signal of a pathological condition. Therefore, it is important to develop alternative, highly sensitive and reliable analytical methodologies to detect and identify this analyte in biological fluids. Herein, we present a proof of concept for the development of a new analytical hybrid platform for IL-6 detection that is based on the combination of drop-coating deposition Raman (DCDR) spectroscopy and graphene-enhanced Raman spectroscopy (GERS) effects. The sensitivity limits for IL-6 detection were found to be a function of the type of substrate used. When a 1 μL droplet of IL-6 solution is deposited and dried on an Si substrate, a DCDR effect occurs, and a detection limit below 1 ng mL-1 is obtained; however, when the same is performed using a hybrid substrate of reduced graphene oxide and silicon (rGO/Si), the joint action of DCDR and GERS effects results in a detection limit well below 1 pg mL-1. It is important to note that this result implies the absolute mass detection of 1 fg of IL-6. In summary, the Raman spectroscopy DCDR/GERS analytical platform proposed here allows the reliable identification of, as well as the very sensitive detection of, IL-6 and promises to improve the performance of clinical evaluations of this biomarker that are currently in use. In this study, the Raman spectra of IL-6 in powder and solution, together with the corresponding band assignment, are presented for the first time in the literature.
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Affiliation(s)
- Emmanuel de la O-Cuevas
- Unidad Académica de Física de La Universidad Autónoma de Zacatecas 98068 Zacatecas Mexico
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México Circuito Externo S/N, Cd. Universitaria 04510 Ciudad de México Mexico
| | - Isidro Badillo-Ramírez
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México Circuito Externo S/N, Cd. Universitaria 04510 Ciudad de México Mexico
| | - Selene R Islas
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México Circuito Externo S/N, Cd. Universitaria 04510 Ciudad de México Mexico
| | - C Araujo-Andrade
- Unidad Académica de Física de La Universidad Autónoma de Zacatecas 98068 Zacatecas Mexico
| | - José M Saniger
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México Circuito Externo S/N, Cd. Universitaria 04510 Ciudad de México Mexico
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19
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Song JY, Larson NR, Thati S, Torres-Vazquez I, Martinez-Rivera N, Subelzu NJ, Leon MA, Rosa-Molinar E, Schöneich C, Forrest ML, Middaugh CR, Berkland CJ. Glatiramer acetate persists at the injection site and draining lymph nodes via electrostatically-induced aggregation. J Control Release 2018; 293:36-47. [PMID: 30414463 DOI: 10.1016/j.jconrel.2018.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 01/01/2023]
Abstract
Glatiramer acetate (GA) is widely prescribed for the treatment of relapsing-remitting multiple sclerosis, however, the mechanism of action is still not fully understood. We investigated the structural properties of GA and examined alterations to the drug upon injection into the subcutaneous space. First, a variety of biophysical characterization techniques were employed to characterize GA in solution. GA was found to exist as alpha helices in solution with a hydrodynamic radius of ~3 nm in size. To simulate GA behavior at the site of injection, GA was injected into a solution of 1.5 MDa hyaluronic acid (HA). Visible aggregates were observed immediately upon injection and subsequent testing indicated aggregation was driven by electrostatic interactions between the positively-charged GA and negatively-charged HA. In vivo testing confirmed GA formed spherical particles in the nano- to micrometer size range, suggesting this mechanism contributes to persistence at the injection site and in draining lymph nodes. The aggregates were found to associate with glycosaminoglycans, suggesting an electrostatic mechanism of induced aggregation like the simulated injection. These novel observations may help explain the complex immunomodulatory mechanisms of GA and adverse injection site reactions seen in patients.
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Affiliation(s)
- Jimmy Y Song
- Department of Pharmaceutical Chemistry, University of Kansas, USA
| | | | - Sharadvi Thati
- Department of Pharmaceutical Chemistry, University of Kansas, USA
| | - Irma Torres-Vazquez
- Microscopy and Analytical Imaging Laboratory, University of Kansas, USA; Department of Pharmacology and Toxicology, University of Kansas, USA
| | - Noraida Martinez-Rivera
- Microscopy and Analytical Imaging Laboratory, University of Kansas, USA; Department of Pharmacology and Toxicology, University of Kansas, USA
| | | | | | - Eduardo Rosa-Molinar
- Department of Bioengineering, University of Kansas, USA; Microscopy and Analytical Imaging Laboratory, University of Kansas, USA; Department of Pharmacology and Toxicology, University of Kansas, USA
| | | | - M Laird Forrest
- Department of Pharmaceutical Chemistry, University of Kansas, USA
| | | | - Cory J Berkland
- Department of Pharmaceutical Chemistry, University of Kansas, USA; Department of Chemistry, University of Kansas, USA; Department of Bioengineering, University of Kansas, USA; Department of Chemical and Petroleum Engineering, University of Kansas, USA.
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20
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018; 57:8519-8524. [DOI: 10.1002/anie.201803234] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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21
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Lipiec E, Perez‐Guaita D, Kaderli J, Wood BR, Zenobi R. Direct Nanospectroscopic Verification of the Amyloid Aggregation Pathway. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ewelina Lipiec
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
- The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences 31-342 Krakow Poland
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - David Perez‐Guaita
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Janina Kaderli
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
| | - Bayden R. Wood
- Centre for Biospectroscopy and School of Chemistry Monash University 3800 Victoria Australia
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences ETH Zurich 8093 Zurich Switzerland
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22
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Herrington WF, Singh GP, Wu D, Barone PW, Hancock W, Ram RJ. Optical Detection of Degraded Therapeutic Proteins. Sci Rep 2018; 8:5089. [PMID: 29572496 PMCID: PMC5865131 DOI: 10.1038/s41598-018-23409-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022] Open
Abstract
The quality of therapeutic proteins such as hormones, subunit and conjugate vaccines, and antibodies is critical to the safety and efficacy of modern medicine. Identifying malformed proteins at the point-of-care can prevent adverse immune reactions in patients; this is of special concern when there is an insecure supply chain resulting in the delivery of degraded, or even counterfeit, drug product. Identification of degraded protein, for example human growth hormone, is demonstrated by applying automated anomaly detection algorithms. Detection of the degraded protein differs from previous applications of machine-learning and classification to spectral analysis: only example spectra of genuine, high-quality drug products are used to construct the classifier. The algorithm is tested on Raman spectra acquired on protein dilutions typical of formulated drug product and at sample volumes of 25 µL, below the typical overfill (waste) volumes present in vials of injectable drug product. The algorithm is demonstrated to correctly classify anomalous recombinant human growth hormone (rhGH) with 92% sensitivity and 98% specificity even when the algorithm has only previously encountered high-quality drug product.
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Affiliation(s)
- William F Herrington
- Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States.
| | - Gajendra P Singh
- Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - Di Wu
- Northeastern University, Boston, Massachusetts, 02115, United States
| | - Paul W Barone
- Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
| | - William Hancock
- Northeastern University, Boston, Massachusetts, 02115, United States
| | - Rajeev J Ram
- Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, United States
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23
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Abstract
Increasingly more and larger structural complexes are being determined
experimentally. The sizes of these systems pose a formidable computational challenge
to the study of their vibrational dynamics by normal mode analysis. To overcome this challenge, this work presents a novel resonance-inspired approach. Tests on large shell structures
of protein capsids demonstrate there is a strong
resonance between the vibrations of a whole capsid and those of individual capsomeres.
We then show how this resonance can be taken advantage of to significantly speed up normal
mode computations.
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Affiliation(s)
- Hyuntae Na
- Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, UNITED STATES
| | - Guang Song
- Computer Science, Iowa State University, 226 Atanasoff Hall, AMES, Iowa, 50010-4844, UNITED STATES
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24
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Pezzotti G, Bock RM, McEntire BJ, Jones E, Boffelli M, Zhu W, Baggio G, Boschetto F, Puppulin L, Adachi T, Yamamoto T, Kanamura N, Marunaka Y, Bal BS. Silicon Nitride Bioceramics Induce Chemically Driven Lysis in Porphyromonas gingivalis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3024-35. [PMID: 26948186 DOI: 10.1021/acs.langmuir.6b00393] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Organisms of Gram-negative phylum bacteroidetes, Porphyromonas gingivalis, underwent lysis on polished surfaces of silicon nitride (Si3N4) bioceramics. The antibacterial activity of Si3N4 was mainly the result of chemically driven principles. The lytic activity, although not osmotic in nature, was related to the peculiar pH-dependent surface chemistry of Si3N4. A buffering effect via the formation of ammonium ions (NH4(+)) (and their modifications) was experimentally observed by pH microscopy. Lysis was confirmed by conventional fluorescence spectroscopy, and the bacteria's metabolism was traced with the aid of in situ Raman microprobe spectroscopy. This latter technique revealed the formation of peroxynitrite within the bacterium itself. Degradation of the bacteria's nucleic acid, drastic reduction in phenilalanine, and reduction of lipid concentration were observed due to short-term exposure (6 days) to Si3N4. Altering the surface chemistry of Si3N4 by either chemical etching or thermal oxidation influenced peroxynitrite formation and affected bacteria metabolism in different ways. Exploiting the peculiar surface chemistry of Si3N4 bioceramics could be helpful in counteracting Porphyromonas gingivalis in an alkaline pH environment.
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Affiliation(s)
- Giuseppe Pezzotti
- Ceramic Physics Laboratory, Kyoto Institute of Technology , Sakyo-ku, Matsugasaki, 606-8126 Kyoto, Japan
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Ryan M Bock
- Amedica Corporation, 1885 West 2100 South, Salt Lake City, Utah 84119, United States
| | - Bryan J McEntire
- Amedica Corporation, 1885 West 2100 South, Salt Lake City, Utah 84119, United States
| | - Erin Jones
- Amedica Corporation, 1885 West 2100 South, Salt Lake City, Utah 84119, United States
| | - Marco Boffelli
- Ceramic Physics Laboratory, Kyoto Institute of Technology , Sakyo-ku, Matsugasaki, 606-8126 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Wenliang Zhu
- Department of Medical Engineering for Treatment of Bone and Joint Disorders, Osaka University , 2-2 Yamadaoka, Suita, Osaka 565-0854, Japan
| | - Greta Baggio
- Ceramic Physics Laboratory, Kyoto Institute of Technology , Sakyo-ku, Matsugasaki, 606-8126 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Francesco Boschetto
- Ceramic Physics Laboratory, Kyoto Institute of Technology , Sakyo-ku, Matsugasaki, 606-8126 Kyoto, Japan
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Leonardo Puppulin
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tetsuya Adachi
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Toshiro Yamamoto
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Narisato Kanamura
- Department of Dental Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - Yoshinori Marunaka
- Department of Molecular Cell Physiology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine , Kamigyo-ku, Kyoto 602-8566, Japan
| | - B Sonny Bal
- Amedica Corporation, 1885 West 2100 South, Salt Lake City, Utah 84119, United States
- Department of Orthopaedic Surgery, University of Missouri , Columbia, Missouri 65212, United States
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Arya S, Kumari A, Dalal V, Bhattacharya M, Mukhopadhyay S. Appearance of annular ring-like intermediates during amyloid fibril formation from human serum albumin. Phys Chem Chem Phys 2015; 17:22862-71. [PMID: 26264974 DOI: 10.1039/c5cp03782d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The self-assembly of proteins triggered by a conformational switch into highly ordered β-sheet rich amyloid fibrils has captivated burgeoning interest in recent years due to the involvement of amyloids in a variety of human diseases and a diverse range of biological functions. Here, we have investigated the mechanism of fibrillogenesis of human serum albumin (HSA), an all-α-helical protein, using an array of biophysical tools that include steady-state as well as time-resolved fluorescence, circular dichroism and Raman spectroscopy in conjunction with atomic force microscopy (AFM). Investigations into the temporal evolution of nanoscale morphology using AFM revealed the presence of ring-like intermediates that subsequently transformed into worm-like fibrils presumably by a ring-opening mechanism. Additionally, a multitude of morphologically-diverse oligomers were observed on the pathway to amyloid formation. Kinetic analysis using multiple structural probes in-tandem indicated that HSA amyloid assembly is a concerted process encompassing a major structural change that is primarily mediated by hydrophobic interactions between thermally-induced disordered segments originating in various domains. A slower growth kinetics of aggregates suggested that the protein structural reorganization is a prerequisite for fibril formation. Moreover, time-dependent Raman spectroscopic studies of HSA aggregation provided key molecular insights into the conformational transitions occurring within the protein amide backbone and at the residue-specific level. Our data revealed the emergence of conformationally-diverse disulfides as a consequence of structural reorganization and sequestration of tyrosines into the hydrophobic amyloid core comprising antiparallel cross β-sheets.
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Affiliation(s)
- Shruti Arya
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research (IISER), Mohali 140306, Punjab, India.
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Žūkienė R, Snitka V. Zinc oxide nanoparticle and bovine serum albumin interaction and nanoparticles influence on cytotoxicity in vitro. Colloids Surf B Biointerfaces 2015; 135:316-323. [PMID: 26275837 DOI: 10.1016/j.colsurfb.2015.07.054] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 07/12/2015] [Accepted: 07/21/2015] [Indexed: 01/08/2023]
Abstract
Bovine serum albumin (BSA) and zinc oxide nanoparticles (ZnO NPs) are chosen as a model system to investigate NPs-protein corona complex formation. ZnO NPs with average size of ∼ 20 nm are coated with BSA using covalent and non-covalent conjugation at temperatures of 4 °C and 20 °C. The interaction mechanism between ZnO NPs and BSA is studied by using UV-vis absorption, fluorescence, synchronous fluorescence and Raman spectroscopy. Raman spectra of BSA in the presence of ZnO NPs are registered for the first time and confirm decreased α-helix content, increased unstructured folding and β-sheet content in BSA structure. The synchronous fluorescence spectra revealed that the hydrophobicity of the tyrosine residue is decreased and that of the tryptophan is increased. The relation of elucidated changes in BSA structure of BSA-coated ZnO NPs cytotoxicity is tested for CHO cell viability and reactive oxygen species (ROS) generation in vitro. Covalent and non-covalent binding of BSA to ZnO NPs reduces ZnO NPs cytotoxicity and ROS generation, however changes in BSA conformation makes corona less protective against ZnO NPs.
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Affiliation(s)
- Rasa Žūkienė
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu 65, Kaunas LT-51369, Lithuania; Department of Biochemistry, Vytautas Magnus University, K. Donelaicio 58, LT-44248 Kaunas, Lithuania
| | - Valentinas Snitka
- Research Center for Microsystems and Nanotechnology, Kaunas University of Technology, Studentu 65, Kaunas LT-51369, Lithuania.
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27
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Chen Y, Dai J, Zhou X, Liu Y, Zhang W, Peng G. Raman spectroscopy analysis of the biochemical characteristics of molecules associated with the malignant transformation of gastric mucosa. PLoS One 2014; 9:e93906. [PMID: 24710050 PMCID: PMC3977959 DOI: 10.1371/journal.pone.0093906] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/10/2014] [Indexed: 11/24/2022] Open
Abstract
Objective The purpose of this study was to comparatively analyze the signature Raman spectra of genomic DNA, nuclei, and tissue of normal gastric mucosa and gastric cancer and to investigate the biochemical transformation of molecules associated with gastric mucosa malignancy. Method Genomic DNA, nuclei, and tissue from normal gastric mucosa and gastric cancer were analyzed by Raman spectroscopy. Results 1) The Raman spectrum of gastric cancer genomic DNA showed that two peaks appeared, one at approximately 1090 cm-1 with a higher intensity than the peak at 1050 cm-1 in the spectrum. Characteristic peaks appeared at 950 cm-1, 1010 cm-1, and 1100-1600 cm-1. 2) Using a hematoxylin and eosin (H&E)-stained section, the intensity of the characteristic peak of nucleic acids at 1085 cm-1 was increased and shifted to 1088 cm-1 in cancer cells. The relative intensity of the characteristic peaks of nucleoproteins at 755 cm-1 and 1607 cm-1 was significantly increased in cancer cells compared with normal cells. 3) Compared with normal tissues, the peak representing PO2- symmetric stretching vibration shifted from 1088 cm-1 to 1083 cm-1 in cancer tissue, and the characteristic peak for collagen at 938 cm-1 shifted to 944 cm-1. In addition, an extra characteristic peak indicating C = C stretching vibration appeared at 1379 cm-1 in the lipid spectrum in cancer tissue. Conclusions The position, intensity, and shape of peaks in the Raman spectra of DNA, nuclei, and tissue from gastric cancer were significantly different compared with those of normal cells. These results indicate that the DNA phosphate backbone becomes unstable in cancer cells and might be broken; the relative content of histones is increased and stable; the relative collagen content is reduced, facilitating cancer cell metastasis; and the relative content of unsaturated fatty acids is increased, increasing the mobility of the plasma membrane of cancer cells.
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Affiliation(s)
- Yao Chen
- Institute of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Jianhua Dai
- Institute of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Xueqian Zhou
- Institute of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Yunjie Liu
- Institute of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
| | - Wei Zhang
- Key Laboratory of Multi-scale Manufacturing Technology, Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, P. R. China
| | - Guiyong Peng
- Institute of Gastroenterology, Southwest Hospital, Third Military Medical University, Chongqing, China
- * E-mail:
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28
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Hung PS, Kuo YC, Chen HG, Chiang HHK, Lee OKS. Detection of osteogenic differentiation by differential mineralized matrix production in mesenchymal stromal cells by Raman spectroscopy. PLoS One 2013; 8:e65438. [PMID: 23734254 PMCID: PMC3667172 DOI: 10.1371/journal.pone.0065438] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 04/24/2013] [Indexed: 11/21/2022] Open
Abstract
Mesenchymal stromal cells (MSCs) hold great potential in skeletal tissue engineering and regenerative medicine. However, conventional methods that are used in molecular biology to evaluate osteogenic differentiation of MSCs require a relatively large amount of cells. Cell lysis and cell fixation are also required and all these steps are time-consuming. Therefore, it is imperative to develop a facile technique which can provide real-time information with high sensitivity and selectivity to detect the osteogenic maturation of MSCs. In this study, we use Raman spectroscopy as a biosensor to monitor the production of mineralized matrices during osteogenic induction of MSCs. In summary, Raman spectroscopy is an excellent biosensor to detect the extent of maturation level during MSCs-osteoblast differentiation with a non-disruptive, real-time and label free manner. We expect that this study will promote further investigation of stem cell research and clinical applications.
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Affiliation(s)
- Pei-San Hung
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Chun Kuo
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - He-Guei Chen
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
| | - Hui-Hua Kenny Chiang
- Institute of Biophotonics, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan
| | - Oscar Kuang-Sheng Lee
- Department of Orthopaedics and Traumatology, Taipei Veterans General Hospital, Taipei, Taiwan
- Stem cell Research Center, National Yang-Ming University, Taipei, Taiwan
- * E-mail:
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