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Rosenberg J, Ischebeck T, Commichau FM. Vitamin B6 metabolism in microbes and approaches for fermentative production. Biotechnol Adv 2016; 35:31-40. [PMID: 27890703 DOI: 10.1016/j.biotechadv.2016.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
Vitamin B6 is a designation for the six vitamers pyridoxal, pyridoxine, pyridoxamine, pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate, and pyridoxamine. PLP, being the most important B6 vitamer, serves as a cofactor for many proteins and enzymes. In contrast to other organisms, animals and humans have to ingest vitamin B6 with their food. Several disorders are associated with vitamin B6 deficiency. Moreover, pharmaceuticals interfere with metabolism of the cofactor, which also results in vitamin B6 deficiency. Therefore, vitamin B6 is a valuable compound for the pharmaceutical and the food industry. Although vitamin B6 is currently chemically synthesized, there is considerable interest on the industrial side to shift from chemical processes to sustainable fermentation technologies. Here, we review recent findings regarding biosynthesis and homeostasis of vitamin B6 and describe the approaches that have been made in the past to develop microbial production processes. Moreover, we will describe novel routes for vitamin B6 biosynthesis and discuss their potential for engineering bacteria that overproduce the commercially valuable substance. We also highlight bottlenecks of the vitamin B6 biosynthetic pathways and propose strategies to circumvent these limitations.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Georg-August-University of Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Crécy-Lagard V. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chem Biol 2016; 11:2304-11. [PMID: 27294475 DOI: 10.1021/acschembio.6b00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DUF1537 is a novel family of kinases identified by comparative genomic approaches. The family is widespread and found in all sequenced plant genomes and 16% of sequenced bacterial genomes. DUF1537 is not a monofunctional family and contains subgroups that can be separated by phylogenetic and genome neighborhood context analyses. A subset of the DUF1537 proteins is strongly associated by physical clustering and gene fusion with the PdxA2 family, demonstrated here to be a functional paralog of the 4-phosphohydroxy-l-threonine dehydrogenase enzyme (PdxA), a central enzyme in the synthesis of pyridoxal-5'-phosphate (PLP) in proteobacteria. Some members of this DUF1537 subgroup phosphorylate l-4-hydroxythreonine (4HT) into 4-phosphohydroxy-l-threonine (4PHT), the substrate of PdxA, in vitro and in vivo. This provides an alternative route to PLP from the toxic antimetabolite 4HT that can be directly generated from the toxic intermediate glycolaldehyde. Although the kinetic and physical clustering data indicate that these functions in PLP synthesis are not the main roles of the DUF1537-PdxA2 enzymes, genetic and physiological data suggest these side activities function has been maintained in diverse sets of organisms.
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Affiliation(s)
- Jennifer J. Thiaville
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Jake Flood
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Svetlana Yurgel
- Dalhousie University, 6299 South
St., Halifax, NS B3H 4R2, Canada
| | - Laurence Prunetti
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | | | - Geoffrey Hutinet
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Farhad Forouhar
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Xinshuai Zhang
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Venkateswaran Ganesan
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Patrick Reddy
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
| | - Oliver Fiehn
- West
Coast Metabolomics Center, UC Davis, Davis, California, United States
- King Abdulaziz University, Biochemistry Department, Jeddah, Saudi Arabia
| | - J. A. Gerlt
- Institute
for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - John F. Hunt
- Department
of Biological Sciences, Columbia University, New York, New York, United States
| | - Shelley D. Copley
- Department
of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado United States
| | - Valérie de Crécy-Lagard
- Department
of Microbiology and Cell Science and Genetic Institute, University of Florida, P.O. Box 110700, Gainesville, Florida 32611-0700, United States
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Rosenberg J, Müller P, Lentes S, Thiele MJ, Zeigler DR, Tödter D, Paulus H, Brantl S, Stülke J, Commichau FM. ThrR, a DNA‐binding transcription factor involved in controlling threonine biosynthesis in
Bacillus subtilis. Mol Microbiol 2016; 101:879-93. [DOI: 10.1111/mmi.13429] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jonathan Rosenberg
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Peter Müller
- Department of GeneticsBacterial Genetics, Friedrich Schiller University JenaJena Germany
| | - Sabine Lentes
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Martin J. Thiele
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | | | - Dominik Tödter
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Henry Paulus
- Boston Biomedical Research InstituteBoston MA USA
| | - Sabine Brantl
- Department of GeneticsBacterial Genetics, Friedrich Schiller University JenaJena Germany
| | - Jörg Stülke
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
| | - Fabian M. Commichau
- Department of General MicrobiologyGeorg August University GöttingenGrisebachstr. 8Göttingen37077 Germany
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Commichau FM, Alzinger A, Sande R, Bretzel W, Reuß DR, Dormeyer M, Chevreux B, Schuldes J, Daniel R, Akeroyd M, Wyss M, Hohmann HP, Prágai Z. Engineering Bacillus subtilis for the conversion of the antimetabolite 4-hydroxy-l-threonine to pyridoxine. Metab Eng 2015; 29:196-207. [DOI: 10.1016/j.ymben.2015.03.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 02/12/2015] [Accepted: 03/05/2015] [Indexed: 11/25/2022]
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Piotrowska DG, Głowacka IE, Wróblewski AE. Stereochemistry of the Three-Component Reaction Between the Ley′S Aldehyde, Benzyl Amines, and Trialkyl Phosphites. A New Approach to the Protected Enantiomerically Pure 1-Amino-2,3-Dihydroxypropylphosphonates. PHOSPHORUS SULFUR 2014. [DOI: 10.1080/10426507.2014.883624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Dorota G. Piotrowska
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Poland
| | - Iwona E. Głowacka
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Poland
| | - Andrzej E. Wróblewski
- Bioorganic Chemistry Laboratory, Faculty of Pharmacy, Medical University of Łódź, Poland
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Commichau FM, Alzinger A, Sande R, Bretzel W, Meyer FM, Chevreux B, Wyss M, Hohmann HP, Prágai Z. Overexpression of a non-native deoxyxylulose-dependent vitamin B6 pathway in Bacillus subtilis for the production of pyridoxine. Metab Eng 2014; 25:38-49. [PMID: 24972371 DOI: 10.1016/j.ymben.2014.06.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/03/2014] [Accepted: 06/18/2014] [Indexed: 12/24/2022]
Abstract
Vitamin B6 is a designation for the vitamers pyridoxine, pyridoxal, pyridoxamine, and their respective 5'-phosphates. Pyridoxal 5'-phosphate, the biologically most-important vitamer, serves as a cofactor for many enzymes, mainly active in amino acid metabolism. While microorganisms and plants are capable of synthesizing vitamin B6, other organisms have to ingest it. The vitamer pyridoxine, which is used as a dietary supplement for animals and humans is commercially produced by chemical processes. The development of potentially more cost-effective and more sustainable fermentation processes for pyridoxine production is of interest for the biotech industry. We describe the generation and characterization of a Bacillus subtilis pyridoxine production strain overexpressing five genes of a non-native deoxyxylulose 5'-phosphate-dependent vitamin B6 pathway. The genes, derived from Escherichia coli and Sinorhizobium meliloti, were assembled to two expression cassettes and introduced into the B. subtilis chromosome. in vivo complementation assays revealed that the enzymes of this pathway were functionally expressed and active. The resulting strain produced 14mg/l pyridoxine in a small-scale production assay. By optimizing the growth conditions and co-feeding of 4-hydroxy-threonine and deoxyxylulose the productivity was increased to 54mg/l. Although relative protein quantification revealed bottlenecks in the heterologous pathway that remain to be eliminated, the final strain provides a promising basis to further enhance the production of pyridoxine using B. subtilis.
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Affiliation(s)
- Fabian M Commichau
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland; Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
| | - Ariane Alzinger
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Rafael Sande
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Werner Bretzel
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Frederik M Meyer
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Bastien Chevreux
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Markus Wyss
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Hans-Peter Hohmann
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland
| | - Zoltán Prágai
- DSM Nutritional Products Ltd., P.O. Box 2676, CH-4002 Basel, Switzerland.
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Schneemann I, Nagel K, Kajahn I, Labes A, Wiese J, Imhoff JF. Comprehensive investigation of marine Actinobacteria associated with the sponge Halichondria panicea. Appl Environ Microbiol 2010; 76:3702-14. [PMID: 20382810 PMCID: PMC2876447 DOI: 10.1128/aem.00780-10] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 04/01/2010] [Indexed: 11/20/2022] Open
Abstract
Representatives of Actinobacteria were isolated from the marine sponge Halichondria panicea collected from the Baltic Sea (Germany). For the first time, a comprehensive investigation was performed with regard to phylogenetic strain identification, secondary metabolite profiling, bioactivity determination, and genetic exploration of biosynthetic genes, especially concerning the relationships of the abundance of biosynthesis gene fragments to the number and diversity of produced secondary metabolites. All strains were phylogenetically identified by 16S rRNA gene sequence analyses and were found to belong to the genera Actinoalloteichus, Micrococcus, Micromonospora, Nocardiopsis, and Streptomyces. Secondary metabolite profiles of 46 actinobacterial strains were evaluated, 122 different substances were identified, and 88 so far unidentified compounds were detected. The extracts from most of the cultures showed biological activities. In addition, the presence of biosynthesis genes encoding polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) in 30 strains was established. It was shown that strains in which either PKS or NRPS genes were identified produced a significantly higher number of metabolites and exhibited a larger number of unidentified, possibly new metabolites than other strains. Therefore, the presence of PKS and NRPS genes is a good indicator for the selection of strains to isolate new natural products.
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Affiliation(s)
- Imke Schneemann
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Kerstin Nagel
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Inga Kajahn
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Antje Labes
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Jutta Wiese
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
| | - Johannes F. Imhoff
- Kieler Wirkstoff-Zentrum (KiWiZ) at the Leibniz Institute of Marine Sciences (IFM-GEOMAR), Am Kiel-Kanal 44, 24106 Kiel, Germany
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Drewke C, Leistner E. Biosynthesis of vitamin B6 and structurally related derivatives. VITAMINS AND HORMONES 2001; 61:121-55. [PMID: 11153264 DOI: 10.1016/s0083-6729(01)61004-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In spite of the rather simple structure of pyridoxal 5'-phosphate (I), a member of the vitamin B6 group, the elucidation of its de novo biosynthesis remained largely unexplored until recently. Experiments designed to investigate the formation of the vitamin B6 pyridine nucleus mainly concentrated on Escherichia coli. The results of tracer experiments with radioactive and stable isotopes, feeding experiments, and molecular biological studies led to the prediction that 4-hydroxy-L-threonine (VIII, R = H) and 1-deoxy-D-xylulose (VII, R = H) are precursors which are assembled to yield the carbon-nitrogen skeleton of vitamin B6. At this point, the involvement of the phosphorylated forms of these precursors in this assembly seems quite clear. However, vitamin B6 biosynthesis in organisms other than E. coli remains largely unknown. Toxic derivatives of vitamin B6, such as ginkgotoxin, occurring in higher plants may be suitable targets to gain further insight into this tricky problem.
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Affiliation(s)
- C Drewke
- Institut für Pharmazeutische Biologie, Rheinische Friedrich-Wilhelms-Universität Bonn, 53115 Bonn, Germany
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Himmeldirk K, Sayer BG, Spenser ID. Comparative Biogenetic Anatomy of Vitamin B1: A 13C NMR Investigation of the Biosynthesis of Thiamin in Escherichia coli and in Saccharomyces cerevisiae. J Am Chem Soc 1998. [DOI: 10.1021/ja973835r] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Klaus Himmeldirk
- Contribution from the Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1
| | - Brian G. Sayer
- Contribution from the Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1
| | - Ian D. Spenser
- Contribution from the Department of Chemistry, McMaster University, Hamilton, Ontario, Canada L8S 4M1
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Drewke C, Notheis C, Hansen U, Leistner E, Hemscheidt T, Hill RE, Spenser ID. Growth response to 4-hydroxy-L-threonine of Escherichia coli mutants blocked in vitamin B6 biosynthesis. FEBS Lett 1993; 318:125-8. [PMID: 8440369 DOI: 10.1016/0014-5793(93)80005-f] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mutants of Escherichia coli (pdx B and pdx C) which are blocked in the biosynthesis of pyridoxol (vitamin B6) showed a growth response to 4-hydroxy-L-threonine. This observation constitutes the first direct evidence in support of the view that 4-hydroxy-L-threonine is implicated in the biosynthesis of vitamin B6. 1-Aminopropan-2,3-diol, the decarboxylation product of 4-hydroxy-L-threonine, does not support the growth of these mutants. Deuterium from deuterium-labelled 1-aminopropan-2,3-diol was not incorporated into pyridoxol.
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Affiliation(s)
- C Drewke
- Institut für Pharmazeutische Biologie, Universität Bonn, Germany
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Hatanaka SI. Amino acids from mushrooms. FORTSCHRITTE DER CHEMIE ORGANISCHER NATURSTOFFE = PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS. PROGRES DANS LA CHIMIE DES SUBSTANCES ORGANIQUES NATURELLES 1992; 59:1-140. [PMID: 1612539 DOI: 10.1007/978-3-7091-9150-7_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- S I Hatanaka
- Department of Biology, College of Arts and Sciences, University of Tokyo, Japan
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Mitchell RE. Implications of toxins in the ecology and evolution of plant pathogenic microorganisms: bacteria. EXPERIENTIA 1991; 47:791-803. [PMID: 1915763 DOI: 10.1007/bf01922459] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This review attempts to rationalise what is known about bacterial phytotoxins and associate it with the ecology and possible evolution of the producing organisms. Study of non-toxin producing variants gives insight into the ecological role of the toxin. Elucidation of chemical structures of phytotoxins has shown that many exist as families of analogous compounds. Studies on the variation of chemical structures and how they are distributed across species and genera can lead to development of hypotheses on evolutionary relationships. Knowledge on biosynthetic pathways to toxins allows recognition of specific enzymatic steps involved in developing the characteristic features of the structures. Phytotoxins often have a potent biochemical activity, and in some cases the producing organism has associated mechanisms to prevent action of the toxin upon itself; in such cases toxigenesis is clearly not a chance event. The various aspects of bacterial toxigenesis indicate that bacterial phytotoxins are special secondary metabolic products that play beneficial roles to the producing organisms in their various ecological niches.
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Affiliation(s)
- R E Mitchell
- DSIR Plant Protection, Mt Albert Research Centre, Auckland, New Zealand
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Shames SL, Ash DE, Wedler FC, Villafranca JJ. Interaction of aspartate and aspartate-derived antimetabolites with the enzymes of the threonine biosynthetic pathway of Escherichia coli. J Biol Chem 1984. [DOI: 10.1016/s0021-9258(17)42554-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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