Comparative analysis of skeleton muscle proteome profile between yak and cattle provides insight into high-altitude adaptation

2020 ◽  
Vol 17 ◽  
Author(s):  
Jin-Wei Xin ◽  
Zhi-Xin Chai ◽  
Cheng-Fu Zhang ◽  
Yu-Mei Yang ◽  
Qiang Zhang ◽  
...  
Keyword(s):  
High Altitude ◽  
Pyruvate Dehydrogenase ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Pyruvate Dehydrogenase Complex ◽  
Pulmonary Arteries ◽  
Adenosine Monophosphate ◽  
Oxygen Utilization ◽  
Antibody Microarray ◽  
Expression Levels

Background:: Mechanisms underlying yak adaptation to high-altitude environments have been investigated at levels of morphology, anatomy, physiology, genome and transcriptome, but not at the proteome level. Objective: To explore for the first time the protein expression profiles in yak to reveal molecular mechanisms underlying adaptation to high altitude, up to now investigated by genome sequencing. Methods: In the present study, an antibody microarray chip was developed, which included 6,500 mouse monoclonal antibodies. Immunoprecipitation and mass spectrometry on 12 selected antibodies showed that the chip was highly specific. Using this chip, muscle tissue proteome was compared between yak and cattle, and 12 significantly differentially expressed proteins (DEPs) were identified and their expression levels were validated by Western blot. Results: Compared with cattle, higher levels of Rieske iron-sulfur protein (RISP), Cytochrome C oxidase subunit 4 isoform 1, mitochondrial (COX4I1), ATP synthase F1 subunit beta (ATP5F1B), Sarcoplasmic/endoplasmic reticulum calcium ATPase1 (SERCA1) and Adenosine monophosphate deaminase1 (AMPD1) in yak might increase oxygen utilization and energy metabolism. Pyruvate dehydrogenase protein X component (PDHX) and Acetyltransferase component of pyruvate dehydrogenase complex (DLAT) showed higher expression levels and L-lactate dehydrogenase A chain (LDHA) showed lower expression level, which might help yak reduce accumulation of lactic acid. In addition, higher expression levels of Filamin C (FLNC) and low levels of AHNAK and Four and a half LIM domains 1(FHL1) in yak might contribute to inhibition of pulmonary arteries vasoconstriction, remodeling and hypertension. Conclusion: Overall, the present study reported new data at protein level in comparison between yak and cattle, which might be helpful to further understand molecular mechanisms underlying yak adaptation to high altitude environments.

Identification of odorant-binding protein genes inGaleruca daurica(Coleoptera: Chrysomelidae) and analysis of their expression profiles

2017 ◽  
Vol 107 (4) ◽  
pp. 550-561 ◽  
Author(s):  
L. Li ◽  
Y.-T. Zhou ◽  
Y. Tan ◽  
X.-R. Zhou ◽  
B.-P. Pang
Keyword(s):  
Amino Acid ◽  
Molecular Mechanisms ◽  
Insect Pests ◽  
Expression Profiles ◽  
Open Reading Frames ◽  
Amino Acid Residues ◽  
Expression Levels ◽  
Molecular Weights ◽  
Related Proteins ◽  
Odorant Binding

AbstractOdorant-binding proteins (OBPs) play a fundamental role in insect olfaction. In recent years,Galeruca daurica(Joannis) (Coleoptera: Chrysomelidae) has become one of the most important insect pests in the Inner Mongolian grasslands of China. This pest only feeds on the species ofAlliumplants, implying the central role of olfaction in its search for specific host plants. However, the olfaction-related proteins have not been investigated in this beetle. In this study, we identified 29 putative OBP genes, namely GdauOBP1–29, from the transcriptome database ofG. dauricaassembled in our laboratory by using RNA-Seq. All 29 genes had the full-length open reading frames except GdauOBP29, encoding proteins in length from 119 to 202 amino acids with their predicted molecular weights from 12 to 22 kDa with isoelectric points from 3.88 to 8.84. Predicted signal peptides consisting of 15–22 amino acid residues were found in all except GdauOBP6, GdauOBP13 and GdauOBP29. The amino acid sequence identity between the 29 OBPs ranged 8.33–71.83%. GdauOBP1–12 belongs to the Classic OBPs, while the others belong with the Minus-C OBPs. Phylogenetic analysis indicated that GdauOBPs are the closest to CbowOBPs fromColaphellus bowringi. RT-PCR and qRT-PCR analyses showed that all GdauOBPs were expressed in adult antennae, 11 of which with significant differences in their expression levels between males and females. Most GdauOBPs were also expressed in adult heads (without antennae), thoraxes, abdomens, legs and wings. Moreover, the expression levels of the GdauOBPs varied during the different development stages ofG. dauricawith most GdauOBPs expressed highly in the adult antennae but scarcely in eggs and pupae. These results provide insights for further research on the molecular mechanisms of chemical communications inG. daurica.

scholarly journals Microstructural Observation and Transcriptome Analysis of Pistil Abortion in ‘Li Guang’ Apricot

2020 ◽  
Author(s):  
Tong Zhao ◽  
Li Cheng ◽  
Cuilian Chen ◽  
De Zhang ◽  
Zhongxing Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Paraffin Section ◽  
Pollen Grains ◽  
Gansu Province ◽  
Signal Molecules ◽  
Rna Seq ◽  
Factors Affecting ◽  
Expression Levels ◽  
Pistil Abortion

Abstract Background: ‘Li Guang’ apricot, a famous local variety, originated in Dunhuang city, Gansu Province,China. It has a long flowering period and a large amount of flowers, but serious pistil abortion has become one of the key factors affecting the fruit set, yield and quality. The distribution and regulation of hormones play an important role in signal molecules of flower abortion. The critical mechanisms of hormone metabolism and the expression levels of genes involved in these processes are, however, poorly understood. Results: To clarify the critical molecular mechanisms of hormone-induced abortion in apricot, normal and abortive flower buds were taken as materials, the pistil abortion of apricot flower was studied by paraffin section, and the RNA seq was used to identify the genes related to flowering regulation. The pistil style was lower than filament. Microstructure showed that the pollen grains of abortive flowers were decreased sharply, the ovaries shrunk and the ovule primordia developed stagnately. Through RNA-Seq, 6647 differentially expressed genes, including 2543 up-regulated and 4104 down-regulated genes, were identified. According to the KEGG Pathway, the pyruvate metabolism, plant hormone signal transduction, spliceosome, RNA transport, protein processing in endoplasmic reticulum and other metabolic pathways were significantly enriched. It revealed that AUX1, AUX / IAA, TIR1, ARF, GH3 and SAUR , vital genes displayed identical differential expression profiles to auxin transduction pathway, and ABF , SnRK2 , PP2C to abscisic acid, JAZ, MYC2 to jasmonic acid. The qRT-PCR assay with independent samples showed that the expression levels of these selected genes were basically consistent with RNA-Seq results. Conclusions : In the whole differentiate stage of flower, pistil abortion represent versatile style . In this process, the changes of hormones play an important role in pistil abortion, especially IAA,GA,and CTK. Related genes involved in hormones synthesis expression regulate the content of hormones and to adapt to the occurrence of pistil abortion under adversity. At the same time, the ethylene response signal factor ERF1/2 (DN70415) was up-regulated in normal flowers, which further indicated that ethylene might be the key regulatory factor affecting the abortion of ‘Liguang’ apricot flowers.

Abstract TP268: Combination Therapy of Normobaric Oxygen With Hypothermia or Ethanol Modulates Pyruvate Dehydrogenase Complex in Thromboembolic Cerebral Ischemia

Stroke ◽  
2016 ◽  
Vol 47 (suppl_1) ◽  
Author(s):  
Alexa Thibodeau ◽  
Lipeng Cai ◽  
Changya Peng ◽  
Xiaokun Geng ◽  
Vicki Diaz ◽  
...  
Keyword(s):  
Combination Therapy ◽  
Protein Expression ◽  
Pyruvate Dehydrogenase ◽  
Pyruvate Dehydrogenase Complex ◽  
Pyruvate Dehydrogenase Kinase ◽  
Tissue Type ◽  
Energy Regulation ◽  
Normobaric Oxygen ◽  
Expression Levels ◽  
Dehydrogenase Complex

Background and Hypothesis: Pyruvate Dehydrogenase Complex (PDH) is a brain mitochondrial matrix enzyme that is inactivated during stroke injury. PDH impairment after stroke can be particularly devastating given PDH’s critical role in the conversion from anaerobic to aerobic energy metabolism. In this study, we evaluated the restoration of oxidative metabolism by measuring reactive oxygen species (ROS) levels and energy regulation by characterizing modulation of PDH and its inhibitor, pyruvate dehydrogenase kinase (PDK), with therapeutic combination of normobaric oxygen (NBO) plus either hypothermia (Hypo) or ethanol (EtOH). Methods: Sprague-Dawley rats were subjected to middle cerebral artery (MCA) occlusion induced with an autologous embolus, the more clinically relevant stroke model. One hour after occlusion, tissue-type plasminogen activator (t-PA) was administered alone or with NBO (60%), EtOH (1.0g/kg) or Hypo (33°C), either singly or in combination. PDH activity and ROS levels were measured at 3 and 24 hours after t-PA administration. Western blotting was used to detect PDH and PDK protein expression levels. Results: Administration of 60% NBO alone after reperfusion by t-PA treatment did not affect PDH activity. Under t-PA, compared to EtOH or Hypo alone, combined administration of NBO plus either EtOH or Hypo produced the greatest increases in PDH activity and protein expression levels, as well as the greatest decrease in PDK expression. Combination therapy also provided the most significant decline in ROS generation compared to any monotherapeutic approach. Conclusions: Reperfusion with t-PA followed by 60% NBO improves the efficacy of EtOH or Hypo in neuroprotection by ameliorating oxidative injury and improving metabolic regulation with PDH. Comparable neuroprotective effects were found when treating with either EtOH or Hypo, suggesting a similar mechanism and the possibility of substituting EtOH for Hypo in the clinical setting.

Equivalence testing in microarray analysis: similarities in the transcriptome of human atherosclerotic and nonatherosclerotic macrophages

2010 ◽  
Vol 41 (3) ◽  
pp. 212-223 ◽  
Author(s):  
Wouter J. Eijgelaar ◽  
Anton J. G. Horrevoets ◽  
Ann-Pascale J. J. Bijnens ◽  
Mat J. A. P. Daemen ◽  
Wim F. J. Verhaegh
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
New Method ◽  
Expression Level ◽  
Marker Genes ◽  
Equivalence Testing ◽  
Expression Levels ◽  
Macrophage Populations

We focus on similarities in the transcriptome of human Kupffer cells and alveolar, splenic, and atherosclerotic plaque-residing macrophages. We hypothesized that these macrophages share a common expression signature. We performed microarray analysis on mRNA from these subsets (4 patients) and developed a novel statistical method to identify genes with significantly similar expression levels. Phenotypic and functional diversity between macrophage subpopulations reflects their plasticity to respond to microenvironmental signals. Apart from detecting differences in expression profiles, the comparison of the transcriptomes of different macrophage populations may also allow the definition of molecular similarities between these subsets. This new method calculates the maximum difference in gene expression level, based on the estimated confidence interval on that gene's expression variance. We listed the genes by equivalence ranking relative to expression level. FDR estimation was used to determine significance. We identified 500 genes with significantly equivalent expression levels in the macrophage subsets at 5.5% FDR using a confidence level of α = 0.05 for equivalence. Among these are the established macrophage marker CD68, IL1 receptor antagonist, and MHC-related CD1C. These 500 genes were submitted to IPA and GO clustering using DAVID. Additionally, hierarchical clustering of these genes in the Novartis human gene expression atlas revealed a subset of 200 genes specifically expressed in macrophages. Equivalently expressed genes, identified by this new method, may not only help to dissect common molecular mechanisms, but also to identify cell- or condition-specific sets of marker genes that can be used for drug targeting and molecular imaging.

scholarly journals Whole-genome resequencing of three Coilia nasus population reveals genetic variations in genes related to immune, vision, migration, and osmoregulation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jun Gao ◽  
Gangchun Xu ◽  
Pao Xu
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genome Resequencing ◽  
Coilia Nasus ◽  
Expression Levels ◽  
Different Populations ◽  
Genome Level ◽  
Whole Genome Resequencing

Abstract Background Coilia nasus is an important anadromous fish, widely distributed in China, Japan, and Korea. Based on morphological and ecological researches of C. nasus, two ecotypes were identified. One is the anadromous population (AP). The sexually mature fish run thousands of kilometers from marine to river for spawning. Another one is the resident population which cannot migrate. Based on their different habitats, they were classified into landlocked population (LP) and sea population (SP) which were resident in the freshwater lake and marine during the entire lifetime, respectively. However, they have never been systematically studied. Moreover, C. nasus is declining sharply due to overfishing and pollution recently. Therefore, further understandings of C. nasus populations are needed for germplasm protection. Results Whole-genome resequencing of AP, LP, and SP were performed to enrich the understanding of different populations of C. nasus. At the genome level, 3,176,204, 3,307,069, and 3,207,906 single nucleotide polymorphisms (SNPs) and 1,892,068, 2,002,912, and 1,922,168 insertion/deletion polymorphisms (InDels) were generated in AP, LP, and SP, respectively. Selective sweeping analysis showed that 1022 genes were selected in AP vs LP; 983 genes were selected in LP vs SP; 116 genes were selected in AP vs SP. Among them, selected genes related to immune, vision, migration, and osmoregulation were identified. Furthermore, their expression profiles were detected by quantitative real-time PCR. Expression levels of selected genes related to immune, and vision in LP were significantly lower than AP and SP. Selected genes related to migration in AP were expressed significantly more highly than LP. Expression levels of selected genes related to osmoregulation were also detected. The expression of NKAα and NKCC1 in LP were significantly lower than SP, while expression of NCC, SLC4A4, NHE3, and V-ATPase in LP was significantly higher than SP. Conclusions Combined to life history of C. nasus populations, our results revealed that the molecular mechanisms of their differences of immune, vision, migration, and osmoregulation. Our findings will provide a further understanding of different populations of C. nasus and will be beneficial for wild C. nasus protection.

scholarly journals Cell Adhesion Molecules in Normal Skin and Melanoma

Biomolecules ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1213
Author(s):  
Cian D’Arcy ◽  
Christina Kiel
Keyword(s):  
Gene Expression ◽  
Cell Adhesion ◽  
Single Cell ◽  
Adhesion Molecules ◽  
Cell Adhesion Molecules ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Cellular Interactions ◽  
Expression Levels ◽  
Skin Physiology

Cell adhesion molecules (CAMs) of the cadherin, integrin, immunoglobulin, and selectin protein families are indispensable for the formation and maintenance of multicellular tissues, especially epithelia. In the epidermis, they are involved in cell–cell contacts and in cellular interactions with the extracellular matrix (ECM), thereby contributing to the structural integrity and barrier formation of the skin. Bulk and single cell RNA sequencing data show that >170 CAMs are expressed in the healthy human skin, with high expression levels in melanocytes, keratinocytes, endothelial, and smooth muscle cells. Alterations in expression levels of CAMs are involved in melanoma propagation, interaction with the microenvironment, and metastasis. Recent mechanistic analyses together with protein and gene expression data provide a better picture of the role of CAMs in the context of skin physiology and melanoma. Here, we review progress in the field and discuss molecular mechanisms in light of gene expression profiles, including recent single cell RNA expression information. We highlight key adhesion molecules in melanoma, which can guide the identification of pathways and strategies for novel anti-melanoma therapies.

scholarly journals Expression Profiles Reveal Involvement of VEGF, IGF1, BIRC5, and MMP1 in Vulvar Carcinogenesis

2021 ◽  
Vol 20 ◽  
pp. 153303382110049
Author(s):  
Tao Zhang ◽  
Qin Liu ◽  
Minghua Yu ◽  
Yibing Lan ◽  
Jianghong Zhou
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Clinical Stage ◽  
Clinicopathological Characteristics ◽  
Gene Expression Omnibus ◽  
Expression Levels ◽  
Key Genes ◽  
Well Differentiated ◽  
New Biomarkers

Objective: The objective of this study was to identify key genes and shed light on the underlying molecular mechanisms of vulvar squamous cell carcinoma (VSCC). Methods: Bioinformatic software was utilized for the identification and characterization of key differentially expressed genes (DEGs) from microarrays GSE63678 and GSE38228, which contain VSCC and normal vulvar tissue data. These microarrays were obtained from Gene Expression Omnibus (GEO). Immunohistochemical assays (55 VSCC and 50 normal vulvar tissues) were utilized to validate the expression of VEGF, IGF1, BIRC5, and MMP1 screened from the identified DEGs. SPSS 18.0 software was used for statistical analyses of the relationships between IGF1, BIRC5, VEGF, MMP1 expression levels and patient clinicopathological characteristics. Results: A total of 141 DEGs were identified, among which 18 genes were closely correlated with the biological characteristics of VSCC. Four of the 18 genes ( VEGF, IGF1, BIRC5, and MMP1) screened from the GEO database were markedly enriched in pathways in cancer ( P < 0.05), and could be considered key genes in VSCC based on KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis in DAVID (Database for Annotation, Visualization and Integrated Discovery).The expression levels of these 4 hub genes, determined by immunohistochemical assays, were consistent with the bioinformatics results. Higher expression of IGF1 showed significant association with well-differentiated carcinomas ( P = 0.017). BIRC5 expression levels showed a positive correlation with clinical stage ( P = 0.039); compared with those in menopause for over 10 years, patients in menopause for less than 10 years at the time of diagnosis tended to have significantly higher expression of BIRC5 ( P = 0.003). VEGF and MMP1 expression levels were not correlated with any of the tested clinicopathological characteristics. Conclusion: VEGF, IGF1, BIRC5, and MMP1 were identified as being associated with VSCC using integrated bioinformatic methods, which may provide important insights into the pathogenesis of this disease and help to identify new biomarkers.

scholarly journals Novel molecular mechanisms involved in hormonal regulation of lactate production in Sertoli cells

Reproduction ◽  
2015 ◽  
Vol 150 (4) ◽  
pp. 311-321 ◽  
Author(s):  
Mariana Regueira ◽  
Silvana Lucía Artagaveytia ◽  
María Noel Galardo ◽  
Eliana Herminia Pellizzari ◽  
Selva Beatriz Cigorraga ◽  
...  
Keyword(s):  
Sertoli Cells ◽  
Pyruvate Dehydrogenase ◽  
Hormonal Regulation ◽  
Molecular Mechanisms ◽  
Pyruvate Dehydrogenase Complex ◽  
Lactate Production ◽  
Pyruvate Dehydrogenase Kinase ◽  
Mrna Levels ◽  
New Information ◽  
Physiological Relevance

The aim of the study was to analyze molecular mechanisms involved in FSH and basic fibroblast growth factor (bFGF) regulation of lactate production in rat Sertoli cells. The regulation of the availability of pyruvate, which is converted to lactate, could be a mechanism utilized by hormones to ensure lactate supply to germ cells. On one hand, the regulation of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase (PFKFB) expression could result in increased glycolysis, while an increase in pyruvate availability may also result from a lower conversion to acetyl-CoA by negative regulation of pyruvate dehydrogenase complex (PDC) activity by phosphorylation. Sertoli cell cultures obtained from 20-day-old rats were used. Stimulation of the cultures with FSH or bFGF showed that FSH increases Pfkfb1 and Pfkfb3 expression while bFGF increases Pfkfb1 mRNA levels. Additionally, we observed that FSH-stimulated lactate production was inhibited in the presence of a PFKFB3 inhibitor, revealing the physiological relevance of this mechanism. As for the regulation of PDC, analysis of pyruvate dehydrogenase kinase (Pdk) expression showed that FSH increases Pdk3 and decreases Pdk4 mRNA levels while bFGF increases the expression of all Pdks. In addition, we showed that bFGF increases phosphorylated PDC levels and that bFGF-stimulated lactate production is partially inhibited in the presence of a PDK inhibitor. Altogether, these results add new information regarding novel molecular mechanisms involved in hormonal regulation of lactate production in Sertoli cells. Considering that lactate is essential for the production of energy in spermatocytes and spermatids, these mechanisms might be relevant in maintaining spermatogenesis and male fertility.

scholarly journals Gene Expression and miRNA Regulation Changes in Leaves of Rice Backcross Introgression Lines

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1381
Author(s):  
Aqin Cao ◽  
Ruihua Wang ◽  
Jianbo Wang
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Introgression Line ◽  
Differentially Expressed ◽  
Mirna Regulation ◽  
Expression Levels ◽  
Expression Of Genes

High-throughput sequencing was used to distinguish the gene and miRNA expression profiles in the leaves of three progenies from a rice backcross introgression line (BC2F12) and their parents (Oryza sativa and wild rice, O. longistaminata). A total of 33,419 genes and 513 miRNAs were identified in two parents and three lines, and the majority of the genes and miRNAs were commonly expressed. The results show that 10.23% to 17.94% of the genes were differentially expressed genes (DEGs) in the progenies compared with those of the two parents, and the majority of them were up-regulated. Of the miRNAs, 12.56% to15.43% were differentially expressed in the progeny/O. sativa comparisons and the majority of which were up-regulated, while 42.02% to 45.21% of miRNAs were differentially expressed in the progeny/O. longistaminata comparisons, of which nearly half were down-regulated. Most of the DEGs and differentially expressed miRNAs showed expression levels close to that of O. sativa, indicating that the expression of genes and miRNAs in progenies was closely related to their chromosome complements and that the miRNAs were more susceptible than the genes to the effects of genomic composition. Furthermore, a larger number of target genes were predicted in the progeny/O. longistaminata comparisons. Finally, we found that the expression of some genes and miRNAs might increase the possibility for abiotic stress responses and adaptation in progenies. Together, our findings increase the understanding of the molecular mechanisms of hybridization and backcrossing on the expression levels of genes and miRNAs in rice leaves.

scholarly journals Identification and Characterization of Dimorphic Expression of Sex-Related Genes in Rock Bream, a Fish With Multiple Sex Chromosomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Huan Li ◽  
Qihui Zhu ◽  
Ruiyi Chen ◽  
Mingtao Liu ◽  
Dongdong Xu
Keyword(s):  
Sex Determination ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Sex Chromosome ◽  
Expression Profiles ◽  
Transcriptional Analysis ◽  
Oplegnathus Fasciatus ◽  
Expression Levels ◽  
Rock Bream ◽  
Dimorphic Expression

The rock bream (Oplegnathus fasciatus) is a typical fish with a unique multiple sex chromosome system. In this study, we investigated the gene expression profiling in the gonads and brains of both males and females using RNA-Seq to identify sex-related genes and pathways. In accordance with the dimorphic expression profiles, combined with Gene ontology and KEGG enrichment analyses, a number of potential genes and pathways associated with sex determination were obtained from transcriptional analysis, especially some sex-biased genes and pathways. Next, we selected 18 candidate genes and analyzed their expression in different tissues and developmental stages. We found that the expression levels of Amh, Dmrt1, Sox9, Dmrtb1, and Nanos2 were significantly higher in the testis than those in the ovary or other tissues, whereas the expression levels of ZP4, Bouncer, RNF208, FoxH1, and TOB were significantly higher in the ovary than those in the testis. Furthermore, the expression levels of these genes in different developmental stages of gonads also showed sexually dimorphic patterns, suggesting that they might play important roles during gonadal development. These genes are useful markers for investigating sex determination and differentiation in rock bream. The findings of this study can provide insights into the molecular mechanisms of sex determination and differentiation in fish with multiple sex chromosome systems.

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