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Zhang L, Wang J, Gu S, Liu X, Hou M, Zhang J, Yang G, Zhao D, Dong R, Gao H. Biosynthesis of D-1,2,4-butanetriol promoted by a glucose-xylose dual metabolic channel system in engineered Escherichia coli. N Biotechnol 2024; 83:26-35. [PMID: 38936658 DOI: 10.1016/j.nbt.2024.06.003] [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: 12/07/2023] [Revised: 05/29/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024]
Abstract
D-1,2,4-butanetriol (BT) is a widely used fine chemical that can be manufactured by engineered Escherichia coli expressing heterologous pathways and using xylose as a substrate. The current study developed a glucose-xylose dual metabolic channel system in an engineered E. coli and Combinatorially optimized it using multiple strategies to promote BT production. The carbon catabolite repression effects were alleviated by deleting the gene ptsG that encodes the major glucose transporter IICBGlc and mutating the gene crp that encodes the catabolite repressor protein, thereby allowing C-fluxes of both glucose and xylose into their respective metabolic channels separately and simultaneously, which increased BT production by 33% compared with that of the original MJ133K-1 strain. Then, the branch metabolic pathways of intermediates in the BT channel were investigated, the transaminase HisC, the ketoreductases DlD, OLD, and IlvC, and the aldolase MhpE and YfaU were identified as the enzymes for the branched metabolism of 2-keto-3-deoxy-xylonate, deletion of the gene hisC increased BT titer by 21.7%. Furthermore, the relationship between BT synthesis and the intracellular NADPH level was examined, and deletion of the gene pntAB that encodes a transhydrogenase resulted in an 18.1% increase in BT production. The combination of the above approaches to optimize the metabolic network increased BT production by 47.5%, resulting in 2.67 g/L BT in 24 deep-well plates. This study provides insights into the BT biosynthesis pathway and demonstrates effective strategies to increase BT production, which will promote the industrialization of the biosynthesis of BT.
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Affiliation(s)
- Lu Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jinbao Wang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Songhe Gu
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Xuedan Liu
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Miao Hou
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jing Zhang
- School of Chemical Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Ge Yang
- School of Life Science, Qufu Normal University, Qufu 273165, Shandong, China
| | - Dongxu Zhao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Runan Dong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Haijun Gao
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.
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2
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Seo PW, Kim GJ, Kim JS. A short guide on blue fluorescent proteins: limits and perspectives. Appl Microbiol Biotechnol 2024; 108:208. [PMID: 38353763 PMCID: PMC10866763 DOI: 10.1007/s00253-024-13012-w] [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: 11/01/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
The advent of the so-called colorful biology era is in line with the discovery of fluorescent proteins (FPs), which can be widely used to detect the intracellular locations of macromolecules or to determine the abundance of metabolites in organelles. The application of multiple FPs that emit different spectra and colors could be implemented to precisely evaluate cellular events. FPs were initially established with the emergence of the green fluorescent protein (GFP) from jellyfish. Red fluorescent proteins (RFPs) from marine anemones and several corals adopt fluorescent chromophores that are similar to GFP. Chromophores of GFP and GFP-like FPs are formed through the oxidative rearrangement of three chromophore-forming residues, thereby limiting their application to only oxidative environments. Alternatively, some proteins can be fluorescent upon their interaction with cellular prosthetic cofactors and, thus, work in aerobic and anaerobic conditions. The modification of an NADPH-dependent blue fluorescent protein (BFP) also expanded its application to the quantization of NADPH in the cellular environment. However, cofactor-dependent BFPs have an intrinsic weakness of poor photostability with a high fluorescent background. This review explores GFP-derived and NADPH-dependent BFPs with a focus on NADPH-dependent BFPs, which might be technically feasible in the near future upon coupling with two-photon fluorescence microscopy or nucleic acid-mimickers. KEY POINTS: • Oxidation-dependent GFP-like BFPs and redox-free NADPH-dependent BFPs • GFPs of weak photostability and intensity with a high fluorescent background • Real-time imaging using mBFP under two-photon fluorescence microscopy.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences, Chonnam National University, Gwangju, 61186, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.
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3
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Šebela M. The use of matrix-assisted laser desorption/ionization mass spectrometry in enzyme activity assays and its position in the context of other available methods. MASS SPECTROMETRY REVIEWS 2023; 42:1008-1031. [PMID: 34549449 DOI: 10.1002/mas.21733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Activity assays are indispensable for studying biochemical properties of enzymes. The purposes of measuring activity are wide ranging from a simple detection of the presence of an enzyme to kinetic experiments evaluating the substrate specificity, reaction mechanisms, and susceptibility to inhibitors. Common activity assay methods include spectroscopy, electrochemical sensors, or liquid chromatography coupled with various detection techniques. This review focuses on the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a growing and modern alternative, which offers high speed of analysis, sensitivity, versatility, possibility of automation, and cost-effectiveness. It may reveal reaction intermediates, side products or measure more enzymes at once. The addition of an internal standard or calculating the ratios of the substrate and product peak intensities and areas overcome the inherent inhomogeneous distribution of analyte and matrix in the sample spot, which otherwise results in a poor reproducibility. Examples of the application of MALDI-TOF MS for assaying hydrolases (including peptidases and β-lactamases for antibiotic resistance tests) and other enzymes are provided. Concluding remarks summarize advantages and challenges coming from the present experience, and draw future perspectives such as a screening of large libraries of chemical compounds for their substrate or inhibitory properties towards enzymes.
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Affiliation(s)
- Marek Šebela
- Department of Biochemistry, Faculty of Science, and CATRIN, Palacký University, Olomouc, Czech Republic
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Vahalová P, Cifra M. Biological autoluminescence as a perturbance-free method for monitoring oxidation in biosystems. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:80-108. [PMID: 36336139 DOI: 10.1016/j.pbiomolbio.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Biological oxidation processes are in the core of life energetics, play an important role in cellular biophysics, physiological cell signaling or cellular pathophysiology. Understanding of biooxidation processes is also crucial for biotechnological applications. Therefore, a plethora of methods has been developed for monitoring oxidation so far, each with distinct advantages and disadvantages. We review here the available methods for monitoring oxidation and their basic characteristics and capabilities. Then we focus on a unique method - the only one that does not require input of additional external energy or chemicals - which employs detection of biological autoluminescence (BAL). We highlight the pros and cons of this method and provide an overview of how BAL can be used to report on various aspects of cellular oxidation processes starting from oxygen consumption to the generation of oxidation products such as carbonyls. This review highlights the application potential of this completely non-invasive and label-free biophotonic diagnostic method.
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Affiliation(s)
- Petra Vahalová
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, 18200, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Prague, 18200, Czech Republic.
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Bahk YY, Ahn SK, Jeon HJ, Na BK, Lee SK, Shin HJ. An Evaluation of a New Quantitative Point-of Care Diagnostic to Measure Glucose-6-phosphate Dehydrogenase Activity. THE KOREAN JOURNAL OF PARASITOLOGY 2022; 60:281-288. [PMID: 36041490 PMCID: PMC9441449 DOI: 10.3347/kjp.2022.60.4.281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022]
Abstract
Malaria continues to be one of the most crucial infectious burdens in endemic areas worldwide, as well as for travelers visiting malaria transmission regions. It has been reported that 8-aminoquinolines are effective against the Plasmodium species, particularly primaquine, for anti-hypnozoite therapy in P. vivax malaria. However, primaquine causes acute hemolytic anemia in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Therefore, G6PD deficiency testing should precede hypnozoite elimination with 8-aminoquinoline. Several point-of-care devices have been developed to detect G6PD deficiency. The aim of the present study was to evaluate the performance of a novel, quantitative G6PD diagnostics based on a metagenomic blue fluorescent protein (mBFP). We comparatively evaluated the sensitivity and specificity of the G6PD diagnostic modality with standard methods using 120 human whole blood samples. The G6PD deficiency was spectrophotometrically confirmed. The performance of the G6PD quantitative test kit was compared with that of a licensed control medical device, the G6PD strip. The G6PD quantitative test kit had a sensitivity of 95% (95% confidence interval (CI): 89.3–100%) and a specificity of 100% (95% CI: 94.3–100%). This study shows that the novel diagnostic G6PD quantitative test kit could be a cost-effective and time-efficient, and universally mandated screening tool for G6PD deficiency.
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Affiliation(s)
- Young Yil Bahk
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju 27478, Korea
| | - Seong Kyu Ahn
- Infectious Diseases Investigation Division, Jeonnam Institute of Public Health and Environment, Muan 58568, Korea
| | - Heung Jin Jeon
- Infection Control Convergence Research Center, Chungnam National University College of Medicine, Deajeon 35015, Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea
| | - Sung-Keun Lee
- Department of Pharmacology, Inha University School of Medicine, Incheon 22212, Korea
- Corresponding authors (; )
| | - Ho-Joon Shin
- Department of Microbiology, Ajou University School of Medicine, Suwon 16499, Korea
- Corresponding authors (; )
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Lee JK, Suh HN, Yoon SH, Lee KH, Ahn SY, Kim HJ, Kim SH. Non-Destructive Monitoring via Electrochemical NADH Detection in Murine Cells. BIOSENSORS 2022; 12:107. [PMID: 35200367 PMCID: PMC8869533 DOI: 10.3390/bios12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Nicotinamide adenine dinucleotide (NADH) is an important cofactor involved in metabolic redox reactions in living cells. The detection of NADH in living animal cells is a challenge. We developed a one-step monitoring method for NADH via an electrocatalytic reaction that uses a surface-modified, screen-printed electrode (SPE) having a redox active monolayer 4'-mercapto-N-phenlyquinone diamine (NPQD) formed by a self-assembled monolayer (SAM) of an aromatic thiol, 4-aminothiophenol (4-ATP). This electrode has a limit of detection (LOD) of 0.49 μM and a sensitivity of 0.0076 ± 0.0006 μM/μA in cell culture media, which indicates that it retains its selectivity. The applicability of this NADH sensor was demonstrated for the first time by cell viability monitoring via NADH-sensing in cell culture supernatants.
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Affiliation(s)
- Ju Kyung Lee
- Department of Medical IT Convergence, Kumoh National Institute of Technology, Gumi 39177, Korea;
| | - Han Na Suh
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
| | - Sung Hoon Yoon
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
- Department of Human and Environmental Toxicology, University of Science & Technology, Daejeon 34113, Korea
| | - Kyu Hong Lee
- Korea Institute of Toxicology, Jeongeup 56212, Korea; (H.N.S.); (S.H.Y.); (K.H.L.)
| | - Sae Young Ahn
- NDD Inc., Gumi 39253, Korea;
- Fuzbien Technology Institute, Rockville, MD 20850, USA
| | - Hyung Jin Kim
- Digital Health Care Research Center, Gumi Electronics and Information Technology Research Institute (GERI), Gumi 39253, Korea;
| | - Sang Hee Kim
- Department of Medical IT Convergence, Kumoh National Institute of Technology, Gumi 39177, Korea;
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7
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Utilization of Spectrochemical Analysis and Diffuse Optical Techniques to Reveal Adulteration of Alike Fish Species and Their Microbial Contamination. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-021-02212-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Špaková I, Dubayová K, Nagyová V, Mareková M. Fluorescence biomarkers of malignant melanoma detectable in urine. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
AbstractMalignant melanoma (MM) is a cancerous transformation of melanocytes. It is a disease with the worst response to therapy and, compared to other malignancies, presents much earlier with metastases. MM still belongs to relatively late-detected malignant diseases. Even so, the MM mortality rate is up to 96% for a relatively small incidence (5%). The gold standard for MM diagnosis is a histopathological examination that requires invasive surgery. An invasive sampling method of a biological material can be a stressful factor for the patient, which is often the reason why patients do not seek medical assistance as soon as possible. Our goal was to find a link between metabolites in urine and the stage of MM. Two excitation peaks at 360–370 nm and 450 nm were characterised in spectra of urine samples. The emission spectra have shown one significant peak at 410–460 nm. After addition of glutathione reductase to the samples, fluorescence dropped down only in patient samples and hidden fluorophores appeared. Malignant diseases are associated with the presence of specific metabolites that can be detected fluorescently in biological material such as urine, which can be a suitable alternative for an early detection of cancer or for tracking changes during and after treatment.
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Affiliation(s)
- Ivana Špaková
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Trieda SNP 1, Košice, 04011, Slovakia
| | - Katarína Dubayová
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Trieda SNP 1, Košice, 04011, Slovakia
| | - Vladimíra Nagyová
- Department of Dermatovenerology, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Košice, 04011, Slovakia
| | - Mária Mareková
- Department of Medical and Clinical Biochemistry, Pavol Jozef Šafárik University in Košice, Faculty of Medicine, Trieda SNP 1, Košice, 04011, Slovakia
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Roshanzadeh A, Kang H, You SH, Park J, Khoa ND, Lee DH, Kim GJ, Kim ES. Real-time monitoring of NADPH levels in living mammalian cells using fluorescence-enhancing protein bound to NADPHs. Biosens Bioelectron 2019; 146:111753. [PMID: 31600627 DOI: 10.1016/j.bios.2019.111753] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/28/2019] [Accepted: 09/30/2019] [Indexed: 01/09/2023]
Abstract
Nicotinamide adenine nucleotide phosphate (NADPH) has been known to be involved in the multiple pathways of cell metabolism. However, conventional quantification assays for NADPH have required breaking down the cell membranes of around one million cells per assay, and monitoring NADPH flux in living cells has been limited by a few available tools. Here, we visualized NADPH levels in human cervical cancer cells HeLa using metagenome-derived blue fluorescent protein (mBFP), which specifically binds to NADPH and enhances the intrinsic fluorescence of NADPH up to 10-fold when imaged by two-photon microscopy to reduce photodamage. Adding an oxidizing agent such as diamide to HeLa cells that expressed mBFP led to an immediate decrease of intracellular NADPH depending on glucose availability in culture media. Furthermore, inhibiting glucose-6-phosphate dehydrogenase (G6PD) in the pentose phosphate pathway with dehydroandrosterone (DHEA) and knockdown of G6PD transcripts gradually decreased NADPH when diamide was added to living cells. These results demonstrate that introducing a bacterial mBFP gene into mammalian cells is a straightforward approach to monitoring intracellular NADPH flux in real time at the single-cell level. Moreover, this strategy can be expanded to tracking the spatio-temporal changes in NADPH even in single-cell organelles such as mitochondria and chloroplasts, which will allow us to more precisely assess the efficacy of biochemically or biophysically metabolic perturbations in animal and plant cells.
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Affiliation(s)
- Amir Roshanzadeh
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Hyuno Kang
- Korea Basic Science Institute Gwangju Center, Gwangju, 61186, Republic of Korea
| | - Sung-Hwan You
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Jaehong Park
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Nguyen Dang Khoa
- School of Biological Sciences and Biotechnology, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Dong-Hyun Lee
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Eung-Sam Kim
- Department of Biological Sciences and Research Center of Ecomimetics, Chonnam National University, Gwangju, 61186, Republic of Korea; Center for Next Generation Sensor Research and Development, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Seo PW, Jo ES, You SH, Cheong DE, Kim GJ, Kim JS. Structure-Guided Generation of a Redox-Independent Blue Fluorescent Protein from mBFP. J Mol Biol 2019; 431:3191-3202. [PMID: 31202883 DOI: 10.1016/j.jmb.2019.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/30/2019] [Accepted: 06/04/2019] [Indexed: 01/24/2023]
Abstract
Fluorescent proteins, such as the green fluorescent protein, are used for detection of cellular components and events. However, green fluorescent protein and its derivatives have limited usage under anaerobic conditions and require a long maturation time. On the other hand, the NADPH-dependent blue fluorescent protein (BFP) without oxidative modification of residues is instantly functional in both aerobic and anaerobic systems. BFP proteins belong to a short-chain dehydrogenase/reductase (SDR) protein family, and their fluorescent property changes with reaction time in the presence of a substrate. With the aim of developing a better fluorescent reporter independent of redox state, we elucidated the crystal structure of a tetrameric mBFP from soil metagenomes with and without NADPH. Apart from the previously known regions, structure-guided mutational studies have identified several residues that contribute to the fluorescence of mBFP, including two aromatic residues (F97 and Y157) near the nicotinamide moiety of the bound NADPH. A single histidine mutation at Y157 (Y157H) has conferred more stabilized, time-independent fluorescence even in the presence of substrates. Furthermore, we discovered another SDR protein that can also emit blue fluorescence. These results open a new possibility for the development of BFP as a stable cellular reporter for widespread use, independent of subcellular environments.
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Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Eun-Seo Jo
- Department of Biological Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sung-Hwan You
- Department of Biological Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Dae-Eun Cheong
- Department of Biological Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Geun-Joong Kim
- Department of Biological Sciences, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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