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Shin SW, Yuk JS, Chun SH, Lim YT, Um SH. Hybrid material of structural DNA with inorganic compound: synthesis, applications, and perspective. NANO CONVERGENCE 2020; 7:2. [PMID: 31903521 PMCID: PMC6943097 DOI: 10.1186/s40580-019-0211-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/01/2019] [Indexed: 05/06/2023]
Abstract
Owing to its precise manipulation in nanoscale, DNA as a genetic code becomes a promising and generic material in lots of nanotechnological outstanding exploitations. The nanoscale assembly of nucleic acids in aqueous solution has showed very remarkable capability that is not achievable from any other material resources. In the meantime, their striking role played by effective intracellular interactions have been identified, making these more attractive for a variety of biological applications. Lately, a number of interesting attempts have been made to augment their marvelous diagnostic and therapeutic capabilities, as being integrated with inorganic compounds involving gold, iron oxide, quantum dot, upconversion, etc. It was profoundly studied how structural DNA-inorganic hybrid materials have complemented with each other in a synergistic way for better-graded biological performances. Such hybrid materials consisting of both structural DNAs and inorganics are gradually receiving much attention as a practical and future-oriented material substitute. However, any special review articles highlighting the significant and innovative materials have yet to be published. At the first time, we here demonstrate novel hybrid complexes made of structural DNAs and inorganics for some practical applications.
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Affiliation(s)
- Seung Won Shin
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
| | - Ji Soo Yuk
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
| | - Sang Hun Chun
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
| | - Yong Taik Lim
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
| | - Soong Ho Um
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419 South Korea
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2
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Frahs S, Reeck JC, Yocham KM, Frederiksen A, Fujimoto K, Scott CM, Beard RS, Brown RJ, Lujan TJ, Solov’yov IA, Estrada D, Oxford JT. Prechondrogenic ATDC5 Cell Attachment and Differentiation on Graphene Foam; Modulation by Surface Functionalization with Fibronectin. ACS APPLIED MATERIALS & INTERFACES 2019; 11:41906-41924. [PMID: 31639302 PMCID: PMC6858527 DOI: 10.1021/acsami.9b14670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 10/22/2019] [Indexed: 05/25/2023]
Abstract
Graphene foam holds promise for tissue engineering applications. In this study, graphene foam was used as a three-dimension scaffold to evaluate cell attachment, cell morphology, and molecular markers of early differentiation. The aim of this study was to determine if cell attachment and elaboration of an extracellular matrix would be modulated by functionalization of graphene foam with fibronectin, an extracellular matrix protein that cells adhere well to, prior to the establishment of three-dimensional cell culture. The molecular dynamic simulation demonstrated that the fibronectin-graphene interaction was stabilized predominantly through interaction between the graphene and arginine side chains of the protein. Quasi-static and dynamic mechanical testing indicated that fibronectin functionalization of graphene altered the mechanical properties of graphene foam. The elastic strength of the scaffold increased due to fibronectin, but the viscoelastic mechanical behavior remained unchanged. An additive effect was observed in the mechanical stiffness when the graphene foam was both coated with fibronectin and cultured with cells for 28 days. Cytoskeletal organization assessed by fluorescence microscopy demonstrated a fibronectin-dependent reorganization of the actin cytoskeleton and an increase in actin stress fibers. Gene expression assessed by quantitative real-time polymerase chain reaction of 9 genes encoding cell attachment proteins (Cd44, Ctnna1, Ctnnb1, Itga3, Itga5, Itgav, Itgb1, Ncam1, Sgce), 16 genes encoding extracellular matrix proteins (Col1a1, Col2a1, Col3a1, Col5a1, Col6a1, Ecm1, Emilin1, Fn1, Hapln1, Lamb3, Postn, Sparc, Spp1, Thbs1, Thbs2, Tnc), and 9 genes encoding modulators of remodeling (Adamts1, Adamts2, Ctgf, Mmp14, Mmp2, Tgfbi, Timp1, Timp2, Timp3) indicated that graphene foam provided a microenvironment conducive to expression of genes that are important in early chondrogenesis. Functionalization of graphene foam with fibronectin modified the cellular response to graphene foam, demonstrated by decreases in relative gene expression levels. These findings illustrate the combinatorial factors of microscale materials properties and nanoscale molecular features to consider in the design of three-dimensional graphene scaffolds for tissue engineering applications.
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Affiliation(s)
- Stephanie
M. Frahs
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
| | - Jonathon C. Reeck
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
| | - Katie M. Yocham
- Department
of Mechanical and Biomedical Engineering, Boise State University, Boise, Idaho 83725, United States
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Anders Frederiksen
- University
of Southern Denmark, Department of Physics,
Chemistry and Pharmacy, Campusvej 55, 5230 Odense M, Denmark
| | - Kiyo Fujimoto
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Crystal M. Scott
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
| | - Richard S. Beard
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
| | - Raquel J. Brown
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
| | - Trevor J. Lujan
- Department
of Mechanical and Biomedical Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Ilia A. Solov’yov
- Department
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky-Straße
9-11, 26129 Oldenburg, Germany
| | - David Estrada
- Micron
School of Materials Science and Engineering, Boise State University, Boise, Idaho 83725, United States
| | - Julia Thom Oxford
- Center
of Biomedical Research Excellence in Matrix Biology, Biomolecular
Research Center, Boise State University, Boise, Idaho 83725, United States
- Department
of Biological Sciences, Boise State University, Boise, Idaho 83725, United States
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3
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Sushko GB, Solov'yov IA, Solov'yov AV. Modeling MesoBioNano systems with MBN Studio made easy. J Mol Graph Model 2019; 88:247-260. [PMID: 30776757 DOI: 10.1016/j.jmgm.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 02/04/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023]
Abstract
This paper introduces MesoBioNano (MBN) Studio - a graphical user interface for a popular multiscale simulation package MBN Explorer. MBN Studio has been developed to facilitate setting up and starting MBN Explorer calculations, monitoring their progress and examining the calculation results. It is tailored for any calculations that are supported by MBN Explorer, such as for example the single-point energy calculations, structure optimization, molecular dynamics, and kinetic Monte Carlo simulations. Apart from that MBN Studio has built-in tools allowing the calculation and analysis of specific characteristics that are determined by the output of the simulations, such as the diffusion coefficients of molecular species, melting temperatures and associated heat capacities, radial distribution function; a dedicated modeling plug-in allows constructing molecular systems in a quick and efficient manner. Employing this plug-in, one can easily construct molecular systems of different geometries (e.g., spherical or ellipsoidal nanoparticles, cubic crystalline samples) with various atomic composition. The paper presents the first public release of MBN Studio and provides an overview of its significant capabilities, as well as the reference point for further extensions.
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Affiliation(s)
- Gennady B Sushko
- MBN Research Center, Altenhöferallee 3, 60438, Frankfurt am Main, Germany.
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
| | - Andrey V Solov'yov
- MBN Research Center, Altenhöferallee 3, 60438, Frankfurt am Main, Germany.
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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Domljanovic I, Rexen Ulven E, Ulven T, Thomsen RP, Okholm AH, Kjems J, Voss A, Taskova M, Astakhova K. Dihydropyridine Fluorophores Allow for Specific Detection of Human Antibodies in Serum. ACS OMEGA 2018; 3:7580-7586. [PMID: 30087918 PMCID: PMC6068599 DOI: 10.1021/acsomega.8b00424] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/26/2018] [Indexed: 05/14/2023]
Abstract
Antigen recognition by antibodies plays an important role in human biology and in the development of diseases. This interaction provides a basis for multiple diagnostic assays and is a guide for treatments. We have developed dihydropyridine-based fluorophores that form stable complexes with double-stranded DNA and upon recognition of the antibodies to DNA (anti-DNA) provide an optical response. The fluorophores described herein have advantageous optical properties compared to those of the currently available dyes making them valuable for research and clinical diagnostics. By studying a series of novel fluorophores, crucial parameters for the design were established, providing the required sensitivity and specificity in the detection of antibodies. Using these DNA-fluorophore complexes in a direct immunofluorescence assay, antibodies to DNA are specifically detected in 80 patients diagnosed with an autoimmune disease, systemic lupus erythematosus. Positivity indicated by emission change of α-(4'-O-methoxyphenyl)-2-furyl dihydropyridine strongly correlates with other disease biomarkers and autoimmune arthritis.
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Affiliation(s)
- Ivana Domljanovic
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Elisabeth Rexen Ulven
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Trond Ulven
- Department
of Drug Design and Pharmacology, University
of Copenhagen, Universitetsparken
2, 2100 Copenhagen, Denmark
| | - Rasmus P. Thomsen
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Anders H. Okholm
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jørgen Kjems
- Interdisciplinary
Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
- Department
of Molecular Biology and Genetics, Aarhus
University, C.F. Møllers
Allé 3, 8000 Aarhus C, Denmark
| | - Anne Voss
- Department
of Rheumatology, Odense University Hospital, J. B. Winsløws Vej 19, 2, 5000 Odense C, Denmark
| | - Maria Taskova
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
| | - Kira Astakhova
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark
- E-mail:
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Samuelsen S, Jørgensen CD, Mellins ED, Torok KS, Astakhova K. Detection of autoimmune antibodies in localized scleroderma by synthetic oligonucleotide antigens. PLoS One 2018; 13:e0195381. [PMID: 29641558 PMCID: PMC5895021 DOI: 10.1371/journal.pone.0195381] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 03/21/2018] [Indexed: 01/08/2023] Open
Abstract
In this study, we developed a series of synthetic oligonucleotides that allowed us to investigate the details on the antigen recognition by autoimmune antibodies in localized scleroderma subjects. Besides dramatically improved analytical specificity of the assay, our data suggests a potential linking for antibodies to DNA to the biological status of disease state in localized scleroderma. Moreover, introducing chemical modifications into short synthetic deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) molecules completely changed the binding titers of corresponding antibodies and their clinical relevance. The strongest observed effect was registered for the localized scleroderma skin damage index (LoSDI) on the IgG antibodies to TC dinucleotide-rich double-stranded antigen (p < 0.001). In addition to providing valuable tools for diagnosis of clinically relevant biomarkers, we believe that this work opens up new opportunities for research on antibodies to nucleic acids in localized scleroderma and other autoimmune diseases.
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Affiliation(s)
- Simone Samuelsen
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden, Denmark
| | | | - Elizabeth D. Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kathryn S. Torok
- Department of Pediatrics, Division of Rheumatology, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Region Hovedstaden, Denmark
- * E-mail:
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7
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Klecka M, Thybo C, Macaubas C, Solov'yov I, Simard J, Balboni IM, Fox E, Voss A, Mellins ED, Astakhova K. Autoantibody Profiling in Lupus Patients using Synthetic Nucleic Acids. Sci Rep 2018; 8:5554. [PMID: 29615791 PMCID: PMC5883037 DOI: 10.1038/s41598-018-23910-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/19/2018] [Indexed: 02/08/2023] Open
Abstract
Autoantibodies to nuclear components of cells (antinuclear antibodies, ANA), including DNA (a-DNA), are widely used in the diagnosis and subtyping of certain autoimmune diseases, including systemic lupus erythematosus (SLE). Despite clinical use over decades, precise, reproducible measurement of a-DNA titers remains difficult, likely due to the substantial sequence and length heterogeneity of DNA purified from natural sources. We designed and tested a panel of synthetic nucleic acid molecules composed of native deoxyribonucleotide units to measure a-DNA. ELISA assays using these antigens show specificity and reproducibility. Applying the ELISA tests to serological studies of pediatric and adult SLE, we identified novel clinical correlations. We also observed preferential recognition of a specific synthetic antigen by antibodies in SLE sera. We determined the probable basis for this finding using computational analyses, providing valuable structural information for future development of DNA antigens. Synthetic nucleic acid molecules offer the opportunity to standardize assays and to dissect antibody-antigen interactions.
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Affiliation(s)
- Martin Klecka
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark
| | - Christina Thybo
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Claudia Macaubas
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA
| | - Ilia Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Julia Simard
- Department of Health and Research Policy, Stanford University School of Medicine, 150 Governor's Lane, Stanford, California, 94305, USA
| | - Imelda Maria Balboni
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Emily Fox
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University, 700 Welch Rd. Suite 301, Stanford, California, 94304, USA
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, J. B. Winsløws Vej 19, 2, 5000, Odense C, Denmark
| | - Elizabeth D Mellins
- Department of Pediatrics, Program in Immunology, Stanford University School of Medicine, 269 Campus Drive, Stanford, California, 94305, USA.
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800, Kgs, Lyngby, Denmark.
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Domljanovic I, Carstens A, Okholm A, Kjems J, Nielsen CT, Heegaard NHH, Astakhova K. Complexes of DNA with fluorescent dyes are effective reagents for detection of autoimmune antibodies. Sci Rep 2017; 7:1925. [PMID: 28507286 PMCID: PMC5432514 DOI: 10.1038/s41598-017-02214-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/06/2017] [Indexed: 11/29/2022] Open
Abstract
To date, there are multiple assays developed that detect and quantify antibodies in biofluids. Nevertheless, there is still a lack of simple approaches that specifically detect autoimmune antibodies to double-stranded DNA. Herein we investigate the potential of novel nucleic acid complexes as targets for these antibodies. This is done in a simple, rapid and specific immunofluorescence assay. Specifically, employing 3D nanostructures (DNA origami), we present a new approach in the detection and study of human antibodies to DNA. We demonstrate the detection of anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We tested the most potent non-covalent pairs of DNA and fluorescent dyes. Several complexes showed specific recognition of autoimmune antibodies in human samples of lupus patients using a simple one-step immunofluorescence method. This makes the novel assay developed herein a promising tool for research and point-of-care monitoring of anti-DNA antibodies. Using this method, we for the first time experimentally confirm that the disease-specific autoimmune antibodies are sensitive to the 3D structure of nucleic acids and not only to the nucleotide sequence, as was previously thought.
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Affiliation(s)
- Ivana Domljanovic
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Annika Carstens
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Anders Okholm
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, 8000, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, 8000, Denmark
| | - Christoffer Tandrup Nielsen
- Copenhagen Lupus and Vasculitis Clinic, Centre for Rheumatology and Spine Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, 2100, Denmark
| | - Niels H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institute, DK-2300, Copenhagen S, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, University of Southern Denmark, DK-5000, Odense C, Denmark
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark.
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