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Engelhardt M, Hintze S, Wendegatz EC, Lettow J, Schüller HJ. Ino2, activator of yeast phospholipid biosynthetic genes, interacts with basal transcription factors TFIIA and Bdf1. Curr Genet 2023; 69:289-300. [PMID: 37947853 PMCID: PMC10716077 DOI: 10.1007/s00294-023-01277-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/24/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Binding of general transcription factors TFIID and TFIIA to basal promoters is rate-limiting for transcriptional initiation of eukaryotic protein-coding genes. Consequently, activator proteins interacting with subunits of TFIID and/or TFIIA can drastically increase the rate of initiation events. Yeast transcriptional activator Ino2 interacts with several Taf subunits of TFIID, among them the multifunctional Taf1 protein. In contrast to mammalian Taf1, yeast Taf1 lacks bromodomains which are instead encoded by separate proteins Bdf1 and Bdf2. In this work, we show that Bdf1 not only binds to acetylated histone H4 but can also be recruited by Ino2 and unrelated activators such as Gal4, Rap1, Leu3 and Flo8. An activator-binding domain was mapped in the N-terminus of Bdf1. Subunits Toa1 and Toa2 of yeast TFIIA directly contact sequences of basal promoters and TFIID subunit TBP but may also mediate the influence of activators. Indeed, Ino2 efficiently binds to two separate structural domains of Toa1, specifically with its N-terminal four-helix bundle structure required for dimerization with Toa2 and its C-terminal β-barrel domain contacting TBP and sequences of the TATA element. These findings complete the functional analysis of yeast general transcription factors Bdf1 and Toa1 and identify them as targets of activator proteins.
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Affiliation(s)
- Maike Engelhardt
- Center for Functional Genomics of Microbes, Institut für Genetik und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Cheplapharm, Greifswald, Germany
| | - Stefan Hintze
- Center for Functional Genomics of Microbes, Institut für Genetik und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
- Friedrich-Baur-Institut an der Neurologischen Klinik und Poliklinik, LMU Klinikum, Munich, Germany
| | - Eva-Carina Wendegatz
- Center for Functional Genomics of Microbes, Institut für Genetik und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Julia Lettow
- Center for Functional Genomics of Microbes, Institut für Genetik und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Hans-Joachim Schüller
- Center for Functional Genomics of Microbes, Institut für Genetik und Funktionelle Genomforschung, Universität Greifswald, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany.
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Müller N, Warwick T, Noack K, Malacarne PF, Cooper AJL, Weissmann N, Schröder K, Brandes RP, Rezende F. Reactive Oxygen Species Differentially Modulate the Metabolic and Transcriptomic Response of Endothelial Cells. Antioxidants (Basel) 2022; 11:antiox11020434. [PMID: 35204316 PMCID: PMC8869421 DOI: 10.3390/antiox11020434] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 02/04/2023] Open
Abstract
Reactive oxygen species (ROS) are important mediators of both physiological and pathophysiological signal transduction in the cardiovascular system. The effects of ROS on cellular processes depend on the concentration, localization, and duration of exposure. Cellular stress response mechanisms have evolved to mitigate the negative effects of acute oxidative stress. In this study, we investigate the short-term and long-term metabolic and transcriptomic response of human umbilical vein endothelial cells (HUVEC) to different types and concentrations of ROS. To generate intracellular H2O2, we utilized a lentiviral chemogenetic approach for overexpression of human D-amino acid oxidase (DAO). DAO converts D-amino acids into their corresponding imino acids and H2O2. HUVEC stably overexpressing DAO (DAO-HUVEC) were exposed to D-alanine (3 mM), exogenous H2O2 (10 µM or 300 µM), or menadione (5 µM) for various timepoints and subjected to global untargeted metabolomics (LC-MS/MS) and RNAseq by MACE (Massive analysis of cDNA ends). A total of 300 µM H2O2 led to pronounced changes on both the metabolic and transcriptomic level. In particular, metabolites linked to redox homeostasis, energy-generating pathways, and nucleotide metabolism were significantly altered. Furthermore, 300 µM H2O2 affected genes related to the p53 pathway and cell cycle. In comparison, the effects of menadione and DAO-derived H2O2 mainly occurred at gene expression level. Collectively, all types of ROS led to subtle changes in the expression of ribosomal genes. Our results show that different types and concentration of ROS lead to a different metabolic and transcriptomic response in endothelial cells.
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Affiliation(s)
- Niklas Müller
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Kurt Noack
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Pedro Felipe Malacarne
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Arthur J. L. Cooper
- Department of Biochemistry and Molecular Biology, New York Medical College, 15 Dana Road, Valhalla, NY 10595, USA;
| | - Norbert Weissmann
- Justus Excellence Cluster Cardio-Pulmonary Institute (CPI), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, 35390 Giessen, Germany;
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
| | - Flávia Rezende
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern Kai 7, 60590 Frankfurt, Germany; (N.M.); (T.W.); (K.N.); (P.F.M.); (K.S.); (R.P.B.)
- German Center of Cardiovascular Research (DZHK), Partner Site Rhein Main, 60590 Frankfurt, Germany
- Correspondence: ; Tel.: +49-69-6301-85321; Fax: +49-69-6301-7668
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Ma SY, Guo YY, Wang SX, Shi JX, Liu J, Liu JF, Zhu P. The T Allele of rs8075977 in the 5'-Flanking Region of the PEDF Gene Is Associated with Reduced Risk of Coronary Artery Disease in Elderly Chinese Men. TOHOKU J EXP MED 2017; 241:297-308. [PMID: 28420811 DOI: 10.1620/tjem.241.297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Coronary artery disease (CAD) is a multifactorial disease with a genetic component. Pigment epithelium-derived factor (PEDF) exerts anti-inflammatory, anti-oxidant, anti-thrombotic, and anti-angiogenic effects and thus has received increasing attention as a sensitive biomarker of atherosclerosis and CAD. To explore the potential association between PEDF single nucleotide polymorphisms (SNPs) and CAD, we performed this case-control study of consecutive elderly Chinese Han male patients (n = 416) and age-matched male controls (n = 528) without a history of CAD or electrocardiographic signs of CAD. The enrolled CAD patients (age ≥ 60 years) are not biologically related. A tag approach was used to examine 100% of common variations in the PEDF gene (r2 ≥ 0.8, minor allele frequency > 0.1). PEDF tag SNPs (tSNPs) were selected using the HapMap Data-CHB which describes the common patterns of human DNA sequence variation and Tagger program. SNPs were genotyped using ligase detection reaction (LDR). Seven tSNPs (rs8075977, rs11658342, rs1136287, rs12603825, rs12453107, rs6828 and rs11078634) were selected. Among them, only one SNP, rs8075977 (C/T) located in the 5'-flanking region, showed the significant effect on the susceptibility to CAD. The frequency of its T allele was significantly higher in the controls (52.7%) than that in the CAD group (46.2%) (adjusted OR = 0.88, 95% CI: 0.80-0.96; P = 0.005). In conclusion, the T allele of rs8075977 in the 5'-flanking region of the PEDF gene may be protective for CAD. Conversely, the C allele at this variation site is associated with CAD in elderly Chinese Han men.
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Affiliation(s)
- Shou-Yuan Ma
- Department of Geriatric Cardiology, Chinese PLA General Hospital
| | - Yuan-Yuan Guo
- Department of Cardiovascular Medicine, Shijingshan Teaching Hospital of Capital Medical University
| | - Shu-Xia Wang
- Department of Cadre Clinic, Chinese PLA General Hospital
| | - Jin-Xin Shi
- Department of Cardiovascular Medicine, Shijingshan Teaching Hospital of Capital Medical University
| | - Jie Liu
- Department of Geriatrics, Civil Aviation General Hospital
| | - Jian-Feng Liu
- Department of Geriatric Cardiology, Chinese PLA General Hospital
| | - Ping Zhu
- Department of Geriatric Cardiology, Chinese PLA General Hospital
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Michoel T, Joshi A, Nachtergaele B, Van de Peer Y. Enrichment and aggregation of topological motifs are independent organizational principles of integrated interaction networks. MOLECULAR BIOSYSTEMS 2011; 7:2769-78. [DOI: 10.1039/c1mb05241a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Gu K, Tian D, Qiu C, Yin Z. Transcription activator-like type III effector AvrXa27 depends on OsTFIIAgamma5 for the activation of Xa27 transcription in rice that triggers disease resistance to Xanthomonas oryzae pv. oryzae. MOLECULAR PLANT PATHOLOGY 2009; 10:829-35. [PMID: 19849788 PMCID: PMC6640403 DOI: 10.1111/j.1364-3703.2009.00567.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The transcription activator-like (TAL) type III effector AvrXa27 from Xanthomonas oryzae pv. oryzae (Xoo) strain PXO99(A) activates the transcription of the host resistance gene Xa27, which results in disease resistance to bacterial blight (BB) in rice. In this study, we show that AvrXa27-activated Xa27 transcription requires host general transcription factor OsTFIIAgamma5. The V39E substitution in OsTFIIAgamma5, encoded by the recessive resistance gene xa5 in rice, greatly attenuates this activation in xa5 and Xa27 double homozygotes on inoculation with Xa27-incompatible strains. The xa5 gene also causes attenuation in the induction of Xa27 by AvrXa27 expressed in rice. The xa5-mediated attenuation of Xa27-mediated resistance to PXO99(A) is recessive. Intriguingly, xa5-mediated resistance to xa5-incompatible strains is also down-regulated in the xa5 and Xa27 double homozygotes. In addition, AvrXa27 expressed in planta shows weak virulence activity in the xa5 genetic background and causes enhanced susceptibility of the plants to BB inoculation. The results suggest that TAL effectors target host general transcription factors to directly manipulate the host transcriptional machinery for virulence and/or avirulence. The identification of xa5-mediated attenuation of Xa27-mediated resistance to Xoo provides a guideline for breeding resistance to BB when pyramiding xa5 with other resistance genes.
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Affiliation(s)
- Keyu Gu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
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Bonham AJ, Neumann T, Tirrell M, Reich NO. Tracking transcription factor complexes on DNA using total internal reflectance fluorescence protein binding microarrays. Nucleic Acids Res 2009; 37:e94. [PMID: 19487241 PMCID: PMC2715255 DOI: 10.1093/nar/gkp424] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We have developed a high-throughput protein binding microarray (PBM) assay to systematically investigate transcription regulatory protein complexes binding to DNA with varied specificity and affinity. Our approach is based on the novel coupling of total internal reflectance fluorescence (TIRF) spectroscopy, swellable hydrogel double-stranded DNA microarrays and dye-labeled regulatory proteins, making it possible to determine both equilibrium binding specificities and kinetic rates for multiple protein:DNA interactions in a single experiment. DNA specificities and affinities for the general transcription factors TBP, TFIIA and IIB determined by TIRF–PBM are similar to those determined by traditional methods, while simultaneous measurement of the factors in binary and ternary protein complexes reveals preferred binding combinations. TIRF–PBM provides a novel and extendible platform for multi-protein transcription factor investigation.
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Affiliation(s)
- Andrew J Bonham
- Department of Biomolecular Science & Engineering, University of California, Santa Barbara, CA, USA
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Abstract
Cap1p, a transcription factor of the basic region leucine zipper family, regulates the oxidative stress response (OSR) in Candida albicans. Alteration of its C-terminal cysteine-rich domain (CRD) results in Cap1p nuclear retention and transcriptional activation. To better understand the function of Cap1p in C. albicans, we used genome-wide location profiling (chromatin immunoprecipitation-on-chip) to identify its transcriptional targets in vivo. A triple-hemagglutinin (HA(3)) epitope was introduced at the C terminus of wild-type Cap1p (Cap1p-HA(3)) or hyperactive Cap1p with an altered CRD (Cap1p-CSE-HA(3)). Location profiling using whole-genome oligonucleotide tiling microarrays identified 89 targets bound by Cap1p-HA(3) or Cap1p-CSE-HA(3) (the binding ratio was at least twofold; P < or = 0.01). Strikingly, Cap1p binding was detected not only at the promoter region of its target genes but also at their 3' ends and within their open reading frames, suggesting that Cap1p may associate with the transcriptional or chromatin remodeling machinery to exert its activity. Overrepresented functional groups of the Cap1p targets (P < or = 0.02) included 11 genes involved in the OSR (CAP1, GLR1, TRX1, SOD1, CAT1, and others), 13 genes involved in response to drugs (PDR16, MDR1, FLU1, YCF1, FCR1, and others), 4 genes involved in phospholipid transport (PDR16, GIT1, RTA2, and orf19.932), and 3 genes involved in the regulation of nitrogen utilization (GST3, orf19.2693, and orf19.3121), suggesting that Cap1p has other cellular functions in addition to the OSR. Bioinformatic analyses of the bound sequences suggest that Cap1p recognizes the DNA motif 5'-MTKASTMA. Finally, transcriptome analyses showed that increased expression generally accompanies Cap1p binding at its targets, indicating that Cap1p functions as a transcriptional activator.
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The Aspergillus fumigatus transcriptional regulator AfYap1 represents the major regulator for defense against reactive oxygen intermediates but is dispensable for pathogenicity in an intranasal mouse infection model. EUKARYOTIC CELL 2007; 6:2290-302. [PMID: 17921349 DOI: 10.1128/ec.00267-07] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Macrophages and neutrophils kill the airborne fungal pathogen Aspergillus fumigatus. The dependency of this killing process on reactive oxygen intermediates (ROI) has been strongly suggested. Therefore, we investigated the enzymatic ROI detoxifying system by proteome analysis of A. fumigatus challenged by H(2)O(2). Since many of the identified proteins and genes are apparently regulated by a putative Saccharomyces cerevisiae Yap1 homolog, the corresponding gene of A. fumigatus was identified and designated Afyap1. Nuclear localization of a functional AfYap1-eGFP fusion was stress dependent. Deletion of the Afyap1 gene led to drastically increased sensitivity of the deletion mutant against H(2)O(2) and menadione, but not against diamide and NO radicals. Proteome analysis of the DeltaAfyap1 mutant strain challenged with 2 mM H(2)O(2) indicated that 29 proteins are controlled directly or indirectly by AfYap1, including catalase 2. Despite its importance for defense against reactive agents, the Afyap1 deletion mutant did not show attenuated virulence in a murine model of Aspergillus infection. These data challenge the hypothesis that ROI such as superoxide anions and peroxides play a direct role in killing of A. fumigatus in an immunocompromised host. This conclusion was further supported by the finding that killing of A. fumigatus wild-type and DeltaAfyap1 mutant germlings by human neutrophilic granulocytes worked equally well irrespective of whether the ROI scavenger glutathione or an NADPH-oxidase inhibitor was added to the cells.
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Mabuchi T, Wakamatsu T, Nakadai T, Shimada M, Yamada K, Matsuda Y, Tamura TA. Chromosomal position, structure, expression, and requirement of genes for chicken transcription factor IIA. Gene 2007; 397:94-100. [PMID: 17544229 DOI: 10.1016/j.gene.2007.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2006] [Revised: 03/14/2007] [Accepted: 04/13/2007] [Indexed: 11/18/2022]
Abstract
Transcription factor IIA (TFIIA) is one of the general transcription factors for RNA polymerase II and composed of three subunits, TFIIAalpha, TFIIAbeta and TFIIAgamma. TFIIAalpha and TFIIAbeta are encoded by a single gene (TFIIAalphabeta) and mature through internal cleavage of TFIIAalphabeta. In this study, we found that structures of TFIIAalphabeta and TFIIAgamma are highly homologous with each mammalian counterpart. Exon-intron organizations of the human and chicken TFIIA genes were also homologous. The sequence of the cleavage region of the chicken TFIIAalphabeta precursor protein was fitted to the consensus cleavage recognition site. It was thus demonstrated that TFIIA is conserved in vertebrates. TFIIA proteins are present ubiquitously in chicken tissues. Fluorescent in situ hybridization revealed that TFIIAalphabeta and TFIIAgamma genes are located in chromosome 5 and a mini-chromosome, respectively. We generated semi-knockout chicken DT40 cells for TFIIAalphabeta and TFIIAgamma genes with high homologous recombination efficiencies, whereas we failed to establish double-knockout cells for each gene. It is thought that both genes for TFIIA are required in vertebrates. TFIIA siRNA resulted in deceleration of cell growth rate, suggesting that, consistent with those of knockout assays, TFIIA is associated with cell growth regulation.
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Affiliation(s)
- Tomoko Mabuchi
- Department of Biology, Faculty of Science, Chiba University, Chiba, Japan
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Iyer-Pascuzzi AS, McCouch SR. Recessive resistance genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae pathosystem. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:731-9. [PMID: 17601161 DOI: 10.1094/mpmi-20-7-0731] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Though recessive resistance is well-studied in viral systems, little is understood regarding the phenomenon in plant-bacterial interactions. The Oryza sativa-Xanthomonas oryzae pv. orzyae pathosystem provides an excellent opportunity to examine recessive resistance in plant-bacterial interactions, in which nine of 30 documented resistance (R) genes are recessively inherited. Infestations of X. oryzae pv. oryzae, the causal agent of bacterial blight, result in significant crop loss and damage throughout South and Southeast Asia. Two recently cloned novel recessive R genes, xa5 and xa13, have yielded insights to this system. Like their viral counterparts, these bacterial recessive R gene products do not conform to the five commonly described classes of R proteins. New findings suggest that such genes may more aptly be viewed as mutations in dominant susceptibility alleles and may also function in a gene-for-gene manner. In this review, we discuss recent accomplishments in the understanding of recessively inherited R genes in the rice-bacterial blight pathosystem and suggest a new model for the function of recessive resistance in plant-bacterial interactions.
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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