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Zare M, Shateri Z, Shakeri M, Nouri M, Zare S, Sarbakhsh P, Eftekhari MH, Gargari BP. The association between diet quality indices and oxidative stress biomarkers in male footballers and healthy active controls. BMC Res Notes 2024; 17:195. [PMID: 39010209 PMCID: PMC11251251 DOI: 10.1186/s13104-024-06858-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: 04/19/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
OBJECTIVE The aim of the present study was the association between the relationship between Dietary Quality Index-International (DQI-I) and Healthy Eating Index (HEI) and the urinary levels of F2alpha-isoprostane (F2a-IP) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) was investigated as indicators of oxidative stress. RESULTS Based on HEI (low, moderate, and good), the diet quality of both groups was classified as moderate. In all participants, HEI (β=-0.29; P = 0.04) and DQI-I (β=-0.46; P = 0.005) were inversely associated with 8-OHdG. Furthermore, a negative correlation was found between HEI (mean β=-3.53; P = 0.04) and DQI-I (mean β=-5.53; P = 0.004) with F2a-IP. The quality of the footballers' diet was higher than that of the control group. Following a high-quality diet, which is rich in antioxidants, is likely to effectively reduce oxidative stress.
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Affiliation(s)
- Mahsa Zare
- Student Research Committee, Faculty of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zainab Shateri
- Department of Nutrition and Biochemistry, School of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Mahboobeh Shakeri
- Endoocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mehran Nouri
- Health Research Institute, Babol University of Medical Sciences, Babol, Iran.
- Health Policy Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Sahar Zare
- Nursing Department, Eghlid Branch, Islamic Azad University, Eghlid, Iran
| | - Parvin Sarbakhsh
- Department of Statistics and Epidemiology, School of Public Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hassan Eftekhari
- Department of Clinical Nutrition, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahram Pourghassem Gargari
- Nutrition Research Center, Department of Biochemistry and Diet Therapy, Faculty of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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Papazoglou A, Henseler C, Weickhardt S, Daubner J, Schiffer T, Broich K, Hescheler J, Sachinidis A, Ehninger D, Haenisch B, Weiergräber M. Sex-specific cortical, hippocampal and thalamic whole genome transcriptome data from controls and a G72 schizophrenia mouse model. BMC Res Notes 2024; 17:143. [PMID: 38773625 PMCID: PMC11110308 DOI: 10.1186/s13104-024-06799-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 05/07/2024] [Indexed: 05/24/2024] Open
Abstract
OBJECTIVES The G72 mouse model of schizophrenia represents a well-known model that was generated to meet the main translational criteria of isomorphism, homology and predictability of schizophrenia to a maximum extent. In order to get a more detailed view of the complex etiopathogenesis of schizophrenia, whole genome transcriptome studies turn out to be indispensable. Here we carried out microarray data collection based on RNA extracted from the retrosplenial cortex, hippocampus and thalamus of G72 transgenic and wild-type control mice. Experimental animals were age-matched and importantly, both sexes were considered separately. DATA DESCRIPTION The isolated RNA from all three brain regions was purified, quantified und quality controlled before initiation of the hybridization procedure with SurePrint G3 Mouse Gene Expression v2 8 × 60 K microarrays. Following immunofluorescent measurement und preprocessing of image data, raw transcriptome data from G72 mice and control animals were extracted and uploaded in a public database. Our data allow insight into significant alterations in gene transcript levels in G72 mice and enable the reader/user to perform further complex analyses to identify potential age-, sex- and brain-region-specific alterations in transcription profiles and related pathways. The latter could facilitate biomarker identification and drug research and development in schizophrenia research.
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Affiliation(s)
- Anna Papazoglou
- Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), Kurt Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Christina Henseler
- Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), Kurt Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Sandra Weickhardt
- Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Johanna Daubner
- Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), Kurt Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Teresa Schiffer
- Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), Kurt Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Karl Broich
- Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
| | - Jürgen Hescheler
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany
- Center of Physiology and Pathophysiology, Faculty of Medicine, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany
| | - Agapios Sachinidis
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany
- Center of Physiology and Pathophysiology, Faculty of Medicine, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany
| | - Dan Ehninger
- Translational Biogerontology, German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE), Venusberg-Campus 1/99, Bonn, 53127, Germany
- German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE), Venusberg-Campus 1/99, Bonn, 53127, Germany
| | - Britta Haenisch
- Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany
- German Center for Neurodegenerative Diseases (Deutsches Zentrum für Neurodegenerative Erkrankungen, DZNE), Venusberg-Campus 1/99, Bonn, 53127, Germany
- Center for Translational Medicine, Medical Faculty, University of Bonn, Bonn, 53113, Germany
| | - Marco Weiergräber
- Experimental Neuropsychopharmacology, Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte, BfArM), Kurt Georg-Kiesinger-Allee 3, Bonn, 53175, Germany.
- Federal Institute for Drugs and Medical Devices (Bundesinstitut für Arzneimittel und Medizinprodukte BfArM), Kurt-Georg-Kiesinger-Allee 3, Bonn, 53175, Germany.
- Faculty of Medicine, Institute of Neurophysiology, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany.
- Center of Physiology and Pathophysiology, Faculty of Medicine, University of Cologne, Robert-Koch-Str. 39, Cologne, 50931, Germany.
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Checkerboard arranged G4 nanostructure-supported electrochemical platform and its application to unique bio-enzymes examination. Bioelectrochemistry 2023; 149:108282. [DOI: 10.1016/j.bioelechem.2022.108282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022]
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Yao L, Liao M, Wang JK, Wang J, Liu D, Tu PF, Zeng KW. Gold Nanoparticle-Based Photo-Cross-Linking Strategy for Cellular Target Identification of Supercomplex Molecular Systems. Anal Chem 2022; 94:3180-3187. [PMID: 35133791 DOI: 10.1021/acs.analchem.1c04652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cellular target identification plays an essential role in innovative drug development and pharmacological mechanism elucidation. However, very few practical experimental methodologies have been developed for identifying target proteins for supercomplex molecular systems such as biologically active phytochemicals or pharmaceutical compositions. To overcome this limitation, we synthesized gold nanoparticles (AuNPs) as solid scaffolds, which were bound with 4,4'-dihydroxybenzophenone (DHBP) as a photo-cross-linking group on the surface. Then, DHBP-modified AuNPs cross-linked various organic compounds from phytochemicals under ultraviolet radiation via carbene reactions, H-C bond insertion, for catalytic C-C bond formation. We next used the phytochemical-cross-linked AuNPs (phytoAuNPs) to pull down potential binding proteins from brain tissue lysate and identified 13 neuroprotective targets by mass spectrometry analysis. As an exemplary study, we selected Hsp60 as a crucial cellular target to further screen 14 target-binding compounds from phytochemicals through surface plasmon resonance (SPR) analysis, followed by Hsp60 activity detection and neuroprotective effect assay in cells. Collectively, this gold nanoparticle-based photo-cross-linking strategy can serve as a useful platform for discovering novel cellular targets for supercomplex molecular systems and help to explore pharmacological mechanisms and active substances.
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Affiliation(s)
- Lu Yao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Min Liao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing-Kang Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Dan Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Peng-Fei Tu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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Chaudhuri R, Fatma K, Dash J. Regulation of gene expression by targeting DNA secondary structures. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Chaudhuri R, Bhattacharya S, Dash J, Bhattacharya S. Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics. J Med Chem 2020; 64:42-70. [PMID: 33355454 DOI: 10.1021/acs.jmedchem.0c01145] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III1 present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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Saha P, Panda D, Müller D, Maity A, Schwalbe H, Dash J. In situ formation of transcriptional modulators using non-canonical DNA i-motifs. Chem Sci 2020; 11:2058-2067. [PMID: 32180928 PMCID: PMC7047845 DOI: 10.1039/d0sc00514b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/28/2020] [Indexed: 12/14/2022] Open
Abstract
Herein, i-motif DNA-immobilized magnetic nanoparticles are used as templates to promote the in situ cycloaddition generating specific binders for i-motifs.
Non-canonical DNA i-motifs and G-quadruplexes are postulated as genetic switches for the transcriptional regulation of proto-oncogenes. However, in comparison to G-quadruplexes, the therapeutic potential of i-motifs is less explored. The development of i-motif selective ligands by conventional approaches is challenging due to the structural complexity of i-motifs. The target guided synthetic (TGS) approach involving in situ cycloaddition could provide specific ligands for these dynamic DNA structures. Herein, we have used i-motif forming C-rich DNA and their complementary G-quadruplex forming DNA sequences of c-MYC and BCL2 promoter regions as well as a control self-complementary duplex DNA sequence as the templates to generate selective ligands from a pool of reactive azide–alkyne building blocks. In our approach, thiolated DNA targets are immobilized on the surface of gold-coated iron nanoparticles to enable efficient isolation of the newly generated ligands from the solution mixture by simple magnetic decantation. The combinatorial in situ cycloaddition generated cell-membrane permeable triazole leads for respective DNA targets (c-MYC and BCL2 i-motifs and G-quadruplexes) that selectively promote their formation. In vitro cellular studies reveal that the c-MYC i-motif and G-quadruplex leads downregulate c-MYC gene expression whereas the BCL2 i-motif lead upregulates and the BCL2 G-quadruplex lead represses BCL2 gene expression. The TGS strategy using i-motif DNA nanotemplates represents a promising platform for the direct in situ formation of i-motif specific ligands for therapeutic intervention.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Deepanjan Panda
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Diana Müller
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Arunabha Maity
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Center for Biomolecular Magnetic Resonance (BMRZ) , Goethe University , Max-von-Laue Strasse 7 , Frankfurt , D-60438 , Germany
| | - Jyotirmayee Dash
- School of Chemical Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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