scholarly journals Expression of Plasmodium vivaxcrt-oIs Related to Parasite Stage but NotEx VivoChloroquine Susceptibility

2015 ◽  
Vol 60 (1) ◽  
pp. 361-367 ◽  
Author(s):  
Zuleima Pava ◽  
Irene Handayuni ◽  
Grennady Wirjanata ◽  
Sheren To ◽  
Leily Trianty ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Ex Vivo ◽  
Drug Susceptibility ◽  
Fold Change ◽  
Low Grade ◽  
Content Type ◽  
Expression Levels ◽  
Stage Of Development ◽  
Parasite Stage

ABSTRACTChloroquine (CQ)-resistantPlasmodium vivaxis present in most countries whereP. vivaxinfection is endemic, but the underlying molecular mechanisms responsible remain unknown. Increased expression ofP. vivaxcrt-o(pvcrt-o) has been correlated within vivoCQ resistance in an area with low-grade resistance. We assessedpvcrt-oexpression in isolates from Papua (Indonesia), whereP. vivaxis highly CQ resistant.Ex vivodrug susceptibilities to CQ, amodiaquine, piperaquine, mefloquine, and artesunate were determined using a modified schizont maturation assay. Expression levels ofpvcrt-owere measured using a novel real-time quantitative reverse transcription-PCR method. Large variations inpvcrt-oexpression were observed across the 51 isolates evaluated, with the fold change in expression level ranging from 0.01 to 59 relative to that seen with theP. vivaxβ-tubulin gene and from 0.01 to 24 relative to that seen with theP. vivaxaldolase gene. Expression was significantly higher in isolates with the majority of parasites at the ring stage of development (median fold change, 1.7) compared to those at the trophozoite stage (median fold change, 0.5;P< 0.001). Twenty-nine isolates fulfilled the criteria forex vivodrug susceptibility testing and showed high variability in CQ responses (median, 107.9 [range, 6.5 to 345.7] nM). After controlling for the parasite stage, we found thatpvcrt-oexpression levels did not correlate with theex vivoresponse to CQ or with that to any of the other antimalarials tested. Our results highlight the importance of development-stage composition for measuringpvcrt-oexpression and suggest thatpvcrt-otranscription is not a primary determinant ofex vivodrug susceptibility. A comprehensive transcriptomic approach is warranted for an in-depth investigation of the role of gene expression levels andP. vivaxdrug resistance.

scholarly journals Cell–cell coupling and DNA methylation abnormal phenotypes in the after-hours mice

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Federico Tinarelli ◽  
Elena Ivanova ◽  
Ilaria Colombi ◽  
Erica Barini ◽  
Edoardo Balzani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Neuronal Networks ◽  
Molecular Mechanisms ◽  
Ex Vivo ◽  
Neuronal Cultures ◽  
Functional Impairments ◽  
After Hours ◽  
The Impact

Abstract Background DNA methylation has emerged as an important epigenetic regulator of brain processes, including circadian rhythms. However, how DNA methylation intervenes between environmental signals, such as light entrainment, and the transcriptional and translational molecular mechanisms of the cellular clock is currently unknown. Here, we studied the after-hours mice, which have a point mutation in the Fbxl3 gene and a lengthened circadian period. Methods In this study, we used a combination of in vivo, ex vivo and in vitro approaches. We measured retinal responses in Afh animals and we have run reduced representation bisulphite sequencing (RRBS), pyrosequencing and gene expression analysis in a variety of brain tissues ex vivo. In vitro, we used primary neuronal cultures combined to micro electrode array (MEA) technology and gene expression. Results We observed functional impairments in mutant neuronal networks, and a reduction in the retinal responses to light-dependent stimuli. We detected abnormalities in the expression of photoreceptive melanopsin (OPN4). Furthermore, we identified alterations in the DNA methylation pathways throughout the retinohypothalamic tract terminals and links between the transcription factor Rev-Erbα and Fbxl3. Conclusions The results of this study, primarily represent a contribution towards an understanding of electrophysiological and molecular phenotypic responses to external stimuli in the Afh model. Moreover, as DNA methylation has recently emerged as a new regulator of neuronal networks with important consequences for circadian behaviour, we discuss the impact of the Afh mutation on the epigenetic landscape of circadian biology.

scholarly journals Antibacterial Mechanism of 405-Nanometer Light-Emitting Diode against Salmonella at Refrigeration Temperature

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Min-Jeong Kim ◽  
Hyun-Gyun Yuk
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Light Emitting Diode ◽  
Dna Oxidation ◽  
Uptake System ◽  
Antibacterial Mechanism ◽  
Content Type ◽  
Light Emitting ◽  
Expression Levels ◽  
Gene Expression Levels

ABSTRACT The aim of this study was to elucidate the antibacterial mechanism of 405 ± 5-nm light-emitting diode (LED) illumination against Salmonella at 4°C in phosphate-buffered saline (PBS) by determining endogenous coproporphyrin content, DNA oxidation, damage to membrane function, and morphological change. Gene expression levels, including of oxyR, recA, rpoS, sodA, and soxR, were also examined to understand the response of Salmonella to LED illumination. The results showed that Salmonella strains responded differently to LED illumination, revealing that S. enterica serovar Enteritidis (ATCC 13076) and S. enterica subsp. enterica serovar Saintpaul (ATCC 9712) were more susceptible and resistant, respectively, than the 16 other strains tested. There was no difference in the amounts of endogenous coproporphyrin in the two strains. Compared with that in nonilluminated cells, the DNA oxidation levels in illuminated cells increased. In illuminated cells, we observed a loss of efflux pump activity, damage to the glucose uptake system, and changes in membrane potential and integrity. Transmission electron microscopy revealed a disorganization of chromosomes and ribosomes due to LED illumination. The levels of the five genes measured in the nonilluminated and illuminated S. Saintpaul cells were upregulated in PBS at a set temperature of 4°C, indicating that increased gene expression levels might be due to a temperature shift and nutrient deficiency rather than to LED illumination. In contrast, only oxyR in S. Enteritidis cells was upregulated. Thus, different sensitivities of the two strains to LED illumination were attributed to differences in gene regulation. IMPORTANCE Bacterial inactivation using visible light has recently received attention as a safe and environmentally friendly technology, in contrast with UV light, which has detrimental effects on human health and the environment. This study was designed to understand how 405 ± 5-nm light-emitting diode (LED) illumination kills Salmonella strains at refrigeration temperature. The data clearly demonstrated that the effectiveness of LED illumination on Salmonella strains depended highly on the serotype and strain. Our findings also revealed that its antibacterial mechanism was mainly attributed to DNA oxidation and a loss of membrane functions rather than membrane lipid peroxidation, which has been proposed by other researchers who studied the antibacterial effect of LED illumination by adding exogenous photosensitizers, such as chlorophyllin and hypericin. Therefore, this study suggests that the detailed antibacterial mechanisms of 405-nm LED illumination without additional photosensitizers may differ from that by exogenous photosensitizers. Furthermore, a change in stress-related gene regulation may alter the susceptibility of Salmonella cells to LED illumination at refrigeration temperature. Thus, our study provides new insights into the antibacterial mechanism of 405 ± 5-nm LED illumination on Salmonella cells.

scholarly journals Harnessing Gene Expression Profiles for the Identification of Ex Vivo Drug Response Genes in Pediatric Acute Myeloid Leukemia

Cancers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1247 ◽  
Author(s):  
David G.J. Cucchi ◽  
Costa Bachas ◽  
Marry M. van den Heuvel-Eibrink ◽  
Susan T.C.J.M. Arentsen-Peters ◽  
Zinia J. Kwidama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drug Resistance ◽  
Drug Response ◽  
Molecular Mechanisms ◽  
Ex Vivo ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Leukemic Cells ◽  
Treatment Optimization ◽  
Pediatric Aml

Novel treatment strategies are of paramount importance to improve clinical outcomes in pediatric AML. Since chemotherapy is likely to remain the cornerstone of curative treatment of AML, insights in the molecular mechanisms that determine its cytotoxic effects could aid further treatment optimization. To assess which genes and pathways are implicated in tumor drug resistance, we correlated ex vivo drug response data to genome-wide gene expression profiles of 73 primary pediatric AML samples obtained at initial diagnosis. Ex vivo response of primary AML blasts towards cytarabine (Ara C), daunorubicin (DNR), etoposide (VP16), and cladribine (2-CdA) was associated with the expression of 101, 345, 206, and 599 genes, respectively (p < 0.001, FDR 0.004–0.416). Microarray based expression of multiple genes was technically validated using qRT-PCR for a selection of genes. Moreover, expression levels of BRE, HIF1A, and CLEC7A were confirmed to be significantly (p < 0.05) associated with ex vivo drug response in an independent set of 48 primary pediatric AML patients. We present unique data that addresses transcriptomic analyses of the mechanisms underlying ex vivo drug response of primary tumor samples. Our data suggest that distinct gene expression profiles are associated with ex vivo drug response, and may confer a priori drug resistance in leukemic cells. The described associations represent a fundament for the development of interventions to overcome drug resistance in AML, and maximize the benefits of current chemotherapy for sensitive patients.

ATF3 and EGR2 gene expression levels in sdLDL-treated macrophages of patients with coronary artery stenosis

2018 ◽  
Vol 42 (1-2) ◽  
pp. 23-29
Author(s):  
Sayed R. Hosseini-Fard ◽  
Mohsen Khosravi ◽  
Amaneh Yarnazari ◽  
Parisa Hassanpour ◽  
Abdollah Amirfarhangi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Coronary Artery ◽  
Cholesterol Metabolism ◽  
Quantitative Polymerase Chain Reaction ◽  
Fold Change ◽  
Expression Level ◽  
Control Group ◽  
Expression Levels ◽  
Vessel Disease ◽  
Gene Expression Levels

AbstractBackground:The metabolism of cholesteryl esters (CEs) is under the control of a gene network in macrophages. Several genes such asATF3andEGR2are related to cholesterol metabolism.Methods:In this study, theATF3andEGR2gene expression levels were evaluated in differentiated macrophages of subjects undergoing coronary artery angiography [controls (<5% stenosis), patients (>70% stenosis)] after treatment with small dense low density lipoprotein (sdLDL) particles. Monocytes were isolated using a RosetteSep Kit and were differentiated into macrophages using the M-CSF factor. A modified heparin-MgSO4-PEG method was used for the sdLDL preparation. TheATF3andEGR2gene expression levels were measured by the real-time quantitative polymerase chain reaction (RT-qPCR) technique.Results:In contrast with the control group (p=0.4), theATF3expression level reduced significantly in the differentiated macrophages from all patients [single vessel disease (SVD), fold change 17 times, p=0.02; two vessel disease (2VD), fold change 1.5 times, p=0.05; three vessel disease (3VD), fold change 3.5 times, p=0.04]. Also, theEGR2expression level reduced significantly in all groups (p<0.02). The gene fold changes had no significant differences between the patients (p>0.8).Conclusions:We propose that the failure ofATF3gene expression improves the CE synthesis after sdLDL influx. Furthermore, the reducedEGR2gene expression level in the sdLDL-treated groups may be a negative factor in cholesterol homeostasis.

scholarly journals Identification of Key Genes and MicroRNAs in Gastric Cancer via miRNA-mRNA Regulatory Network

2020 ◽  
Author(s):  
Chao Huang ◽  
Xiaojian Zhu ◽  
Jiefeng Zhao ◽  
Fanqin Bu ◽  
Jun Huang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gastric Cancer ◽  
Molecular Markers ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Critical Role ◽  
Differentially Expressed ◽  
Expression Levels ◽  
Receptor Interactions

Abstract Background Gastric cancer (GC) is a malignant tumor with high mortality. MicroRNAs (miRNAs) participate in various biological processes and disease pathogenesis by targeting messenger RNA (mRNA). The purpose of this study was to identify potential prognostic molecular markers of GC and to characterize the molecular mechanisms of GC. Methods A gene expression profiling dataset (GSE54129) and miRNA expression profiling dataset (GSE113486) were downloaded from the Gene Expression Omnibus (GEO) database. A miRNA-mRNA interaction network was established. Functional and pathway enrichment analyses were performed for differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) using FunRich, the clusterProfiler package, and DIANA-mirPath. Survival analysis of key molecular markers was performed using the online tool Kaplan-Meier Plotter and the database OncomiR. Finally, experiments were carried out to verify the expression levels and biological functions of a key gene. Results A total of 390 DEMs and 341 DEGs were identified. Ultimately, 45 genes and 31 miRNAs were selected to establish a miRNA-mRNA regulatory network. Four hub genes (ZFPM2, FUT9, NEUROD1 and LIPH) and six miRNAs (hsa-let-7d-5p, hsa-miR-23b-3p, hsa-miR-23a-3p, hsa-miR-133b, hsa-miR-130a-3p and hsa-miR-124-3p) were identified in the network. DEGs and DEMs were associated with ECM-receptor interactions and metabolic pathways. Two genes (ZFPM2 and LIPH) and two miRNAs (hsa-miR-23a-3p and hsa-miR-130a-3p) were observed to be related to the prognosis of GC. ZFPM2 was highly expressed in GC tissues and various GC cell lines and could promote the proliferation, invasion and migration of GC cells. Conclusion The expression levels of ZFPM2, LIPH, hsa-miR-23a-3p and hsa-miR-130a-3p were closely related to the prognosis of GC. ZFPM2 may serve as a potential molecular marker and therapeutic target for GC. ECM receptor interactions and metabolic abnormalities play a critical role in the GC progression.

scholarly journals High Expression of Glycolytic Genes in Clinical Glioblastoma Patients Correlates with Lower Survival

2021 ◽  
Author(s):  
Kimberly M Stanke ◽  
Carrick Wilson ◽  
Srivatsan Kidambi
Keyword(s):  
Gene Expression ◽  
Aerobic Glycolysis ◽  
Treatment Options ◽  
Lactate Production ◽  
Tca Cycle ◽  
Metabolic Reprogramming ◽  
High Expression ◽  
Low Grade ◽  
Normal Brain ◽  
Expression Levels

Glioblastoma (GBM), the most aggressive brain tumor, is associated with a median survival at diagnosis of 16-20 months and limited treatment options. The key hallmark of GBM is altered tumor metabolism and marked increase in the rate of glycolysis. Aerobic glycolysis along with elevated glucose consumption and lactate production supports rapid cell proliferation and GBM growth. In this study, we examined the gene expression profile of metabolic targets in GBM samples from patients with low grade glioma (LGG) and GBM. We found that gene expression of glycolytic enzymes is up-regulated in GBM samples and significantly associated with an elevated risk for developing GBM. Our findings of clinical outcomes showed that GBM patients with high expression of HK2 and PKM2 in the glycolysis related genes and low expression of genes involved in mitochondrial metabolism-SDHB and COX5A related to tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS), respectively, was associated with poor patient overall survival. Surprisingly, expression levels of genes involved in mitochondrial oxidative metabolism are markedly increased in GBM compared to LGG but was lower compared to normal brain. The fact that in GBM the expression levels of TCA cycle and OXPHOS-related genes are higher than those in LGG patients suggests the metabolic shift in GBM cells when progressing from LGG to GBM. These results are an important step forward in our understanding of the role of metabolic reprogramming in glioma as drivers of the tumor and could be potential prognostic targets in GBM therapies.

scholarly journals Genetic Variants Associated mRNA Stability in Lung

2021 ◽  
Author(s):  
Jian-Rong Li ◽  
Mabel Tang ◽  
Yafang Li ◽  
Christopher I Amos ◽  
Chao Cheng
Keyword(s):  
Gene Expression ◽  
Mrna Stability ◽  
Genetic Variants ◽  
Molecular Mechanisms ◽  
Rna Binding ◽  
Tissue Expression ◽  
Rna Seq ◽  
Genetic Traits ◽  
Expression Levels ◽  
Gene Expression Levels

Abstract Background: Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs).Results: Here, we presented a computational framework that take the advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3,942 genes and 186,132 eQTLs for 4,751 genes from 15,122,700 genetic variants for 13,476 genes, respectively. Interesting, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels.

scholarly journals Identification of EP300 as a Key Gene Involved in Antipsychotic-Induced Metabolic Dysregulation Based on Integrative Bioinformatics Analysis of Multi-Tissue Gene Expression Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Albert Martínez-Pinteño ◽  
Patricia Gassó ◽  
Llucia Prohens ◽  
Alex G. Segura ◽  
Mara Parellada ◽  
...  
Keyword(s):  
Gene Expression ◽  
Molecular Mechanisms ◽  
Gene Set Enrichment Analysis ◽  
Metabolic Effects ◽  
First Episode ◽  
Hormone Regulation ◽  
Metabolic Abnormalities ◽  
Expression Levels ◽  
Cholesterol Levels ◽  
Mouse Tissues

Antipsychotics (APs) are associated with weight gain and other metabolic abnormalities such as hyperglycemia, dyslipidemia and metabolic syndrome. This translational study aimed to uncover the underlying molecular mechanisms and identify the key genes involved in AP-induced metabolic effects. An integrative gene expression analysis was performed in four different mouse tissues (striatum, liver, pancreas and adipose) after risperidone or olanzapine treatment. The analytical approach combined the identification of the gene co-expression modules related to AP treatment, gene set enrichment analysis and protein-protein interaction network construction. We found several co-expression modules of genes involved in glucose and lipid homeostasis, hormone regulation and other processes related to metabolic impairment. Among these genes, EP300, which encodes an acetyltransferase involved in transcriptional regulation, was identified as the most important hub gene overlapping the networks of both APs. Then, we explored the genetically predicted EP300 expression levels in a cohort of 226 patients with first-episode psychosis who were being treated with APs to further assess the association of this gene with metabolic alterations. The EP300 expression levels were significantly associated with increases in body weight, body mass index, total cholesterol levels, low-density lipoprotein cholesterol levels and triglyceride concentrations after 6 months of AP treatment. Taken together, our analysis identified EP300 as a key gene in AP-induced metabolic abnormalities, indicating that the dysregulation of EP300 function could be important in the development of these side effects. However, more studies are needed to disentangle the role of this gene in the mechanism of action of APs.

scholarly journals Gene expression levels of DNA methyltransferase enzymes in Shank3-deficient mouse model of autism during early development

2021 ◽  
Vol 55 (4) ◽  
pp. 234-237
Author(s):  
Annamaria Srancikova ◽  
Alexandra Reichova ◽  
Zuzana Bacova ◽  
Jan Bakos
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Brain Development ◽  
Early Development ◽  
Molecular Mechanisms ◽  
Altered Expression ◽  
Expression Levels ◽  
The Brain ◽  
Deficient Mice ◽  
Gene Expression Levels

Abstract Objectives. The balance between DNA methylation and demethylation is crucial for the brain development. Therefore, alterations in the expression of enzymes controlling DNA methylation patterns may contribute to the etiology of neurodevelopmental disorders, including autism. SH3 and multiple ankyrin repeat domains 3 (Shank3)-deficient mice are commonly used as a well-characterized transgenic model to investigate the molecular mechanisms of autistic symptoms. DNA methyltransferases (DNMTs), which modulate several cellular processes in neurodevelopment, are implicated in the pathophysiology of autism. In this study, we aimed to describe the gene expression changes of major Dnmts in the brain of Shank3-deficient mice during early development. Methods and Results. The Dnmts gene expression was analyzed by qPCR in 5-day-old homo-zygous Shank3-deficient mice. We found significantly lower Dnmt1 and Dnmt3b gene expression levels in the frontal cortex. However, no such changes were observed in the hippocampus. However, significant increase was observed in the expression of Dnmt3a and Dnmt3b genes in the hypothalamus of Shank3-deficient mice. Conclusions. The present data indicate that abnormalities in the Shank3 gene are accompanied by an altered expression of DNA methylation enzymes in the early brain development stages, therefore, specific epigenetic control mechanisms in autism-relevant models should be more extensively investigated.

scholarly journals Differences in articular hip cartilage gene expression between femoroacetabular impingement (FAI) and end-stage hip osteoarthritis

2020 ◽  
Vol 8 (7_suppl6) ◽  
pp. 2325967120S0039
Author(s):  
John Reuter ◽  
Gillian Soles ◽  
Cheryl Ackert-Bicknell ◽  
Brian Giordano ◽  
Benjamin Kuhns
Keyword(s):  
Gene Expression ◽  
Femoral Head ◽  
Differential Expression ◽  
Rna Sequencing ◽  
Femoroacetabular Impingement ◽  
Molecular Mechanisms ◽  
Hip Osteoarthritis ◽  
Fold Change ◽  
Cam Deformity ◽  
End Stage

Objectives: The morphological deformities in Femoroacetabular Impingement (FAI) have been associated with hip osteoarthritis (OA), however the molecular mechanisms for OA initiation and progression are poorly understood. The purpose of this study was to use whole genome RNA sequencing to characterize differences in gene expression articular cartilage samples isolated from patients undergoing surgery for FAI and idiopathic OA. We hypothesized that there would be significant differences in genes expression in pathways related to inflammation as well as cartilage and bone turnover. Methods: 20 patients undergoing either hip arthroscopy for FAI (5 male, 5 female) or total hip arthroplasty (5 male, 5 female) for end-stage osteoarthritis were included in the study. FAI patients required a Cam deformity with an Alpha Angle greater than 55 while patients with dysplasia (LCEA<25) or prior hip surgery were excluded. Exclusion criteria for the THA cohort included dysplasia, and post-traumatic OA or inflammatory OA. Cartilage samples were obtained over the Cam deformity prior to femoroplasty in the FAI group or over anterosuperior femoral head-neck junction in the OA group following extraction of the femoral head. Following RNA isolation, Next Generation RNA sequencing was performed to evaluate gene expression. Differential expression data was incorporated into the Ingenuity Pathway Analysis (IPA) platform to identify differences in canonical signaling pathways associated with osteoarthritis. Results: There were 3531 genes that were significantly differentially expressed between the FAI and OA cohorts. Of these, there were 27 genes that were upregulated by a greater than 2 log-fold change in the OA cohort and 524 genes that were upregulated by a greater than 2 log-fold change in the FAI cohort. There was significant differential expression in genes related to cartilage metabolism (Table 1) and canonical osteoarthritis pathways involving BMP, TGFβ, and Wnt signaling. (Table 2). Additionally, FAI samples had significant upregulation of EGF-ERBB mediated signaling which compared to osteoarthritic tissue. Conclusion: The results of the present study support our hypothesis that there are significant differences in gene expression between FAI and OA samples in multiple pathways that are implicated in osteoarthritis. Osteoarthritis samples had increased expression of cartilage breakdown and inflammation while femoroacetabular impingement samples had greater expression of chondroprotective genes. Further study of cartilage samples from FAI patients may provide insight into the molecular mechanisms of osteoarthritis progression. [Table: see text][Table: see text]

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