Publications by authors named "Yulia Skvortsova"

15 Publications

  • Page 1 of 1

Small RNA MTS1338 Confers Pathogenic Properties to Non-Pathogenic .

Microorganisms 2021 Feb 17;9(2). Epub 2021 Feb 17.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia.

Small non-coding RNAs play a key role in bacterial adaptation to various stresses. small RNA MTS1338 is upregulated during mycobacteria infection of macrophages, suggesting its involvement in the interaction of the pathogen with the host. In this study, we explored the functional effects of MTS1338 by expressing it in non-pathogenic that lacks the MTS1338 gene. The results indicated that MTS1338 slowed the growth of the recombinant mycobacteria in culture and increased their survival in RAW 264.7 macrophages, where the MTS1338-expressing strain significantly ( < 0.05) reduced the number of mature phagolysosomes and changed the production of cytokines IL-1β, IL-6, IL-10, IL-12, TGF-β, and TNF-α compared to those of the control strain. Proteomic and secretomic profiling of recombinant and control strains revealed differential expression of proteins involved in the synthesis of main cell wall components and in the regulation of iron metabolism (ESX-3 secretion system) and response to hypoxia (). These effects of MTS1338 expression are characteristic for during infection, suggesting that in pathogenic mycobacteria MTS1338 plays the role of a virulence factor supporting the residence of in the host.
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http://dx.doi.org/10.3390/microorganisms9020414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7921967PMC
February 2021

MTS1338, A Small RNA, Regulates Transcriptional Shifts Consistent With Bacterial Adaptation for Entering Into Dormancy and Survival Within Host Macrophages.

Front Cell Infect Microbiol 2019 26;9:405. Epub 2019 Nov 26.

Laboratory of Regulatory Transcriptomics, Department of Genomics and Postgenomic Technologies, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.

Small non-coding RNAs play a significant role in bacterial adaptation to changing environmental conditions. We investigated the dynamics of expression of MTS1338, a small non-coding RNA of , in the mouse model , regulation of its expression in the infected macrophages, and the consequences of its overexpression in bacterial cultures. Here we demonstrate that MTS1338 significantly contributes to host-pathogen interactions. Activation of the host immune system triggered NO-inducible up-regulation of MTS1338 in macrophage-engulfed mycobacteria. Constitutive overexpression of MTS1338 in cultured mycobacteria improved their survival under low pH conditions. MTS1338 up-regulation launched a spectrum of shifts in the transcriptome profile similar to those reported for adaptation to hostile intra-macrophage environment. Using the RNA-seq approach, we demonstrate that gene expression changes accompanying MTS1338 overexpression indicate reduction in translational activity and bacterial growth. These changes indicate mycobacteria entering the dormant state. Taken together, our results suggest a direct involvement of this sRNA in the interplay between mycobacteria and the host immune system during infectious process.
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http://dx.doi.org/10.3389/fcimb.2019.00405DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901956PMC
August 2020

A New Antisense Phosphoryl Guanidine Oligo-2'-O-Methylribonucleotide Penetrates Into Intracellular Mycobacteria and Suppresses Target Gene Expression.

Front Pharmacol 2019 19;10:1049. Epub 2019 Sep 19.

Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

The worldwide spread of multidrug-resistant strains prompted the development of new strategies to combat tuberculosis, one of which is antisense therapy based on targeting bacterial mRNA by oligonucleotide derivatives. However, the main limitation of antisense antibacterials is poor cellular uptake because of electrostatic charge. Phosphoryl guanidine oligo-2'--methylribonucleotides (2'-OMe PGOs) are a novel type of uncharged RNA analogues with high RNA affinity, which penetrate through the bacterial cell wall more efficiently. In this study, we investigated the uptake and biological effects of 2'-OMe PGO in mycobacteria. The results indicated that 2'-OMe PGO specific for the alanine dehydrogenase-encoding gene inhibited the growth of and downregulated expression at both the transcriptional and translational levels through an RNase H-independent mechanism, showing higher biological activity than its phosphorothioate oligonucleotide counterpart. Confocal microscopy revealed that the anti- 2'-OMe PGO was taken up by intracellular mycobacteria residing in RAW 264.7 macrophages without exerting toxic effects on eukaryotic cells, indicating that 2'-OMe PGO was able to efficiently cross two cellular membranes. In addition, 2'-OMe PGO inhibited the transcription of the target gene in -infected macrophages. Thus, we demonstrated, for the first time, a possibility of targeting gene expression and inhibiting growth of intracellular mycobacteria by antisense oligonucleotide derivatives. Strong antisense activity and efficient uptake of the new RNA analogue, 2'-OMe PGO, by intracellular microorganisms revealed here may promote the development of novel therapeutic strategies to treat TB and prevent the emergence of drug-resistant mycobacterial strains.
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http://dx.doi.org/10.3389/fphar.2019.01049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778816PMC
September 2019

Resuscitation of Dormant "Non-culturable" Is Characterized by Immediate Transcriptional Burst.

Front Cell Infect Microbiol 2019 30;9:272. Epub 2019 Jul 30.

Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia.

Under unfavorable conditions such as host immune responses and environmental stresses, human pathogen may acquire the dormancy phenotype characterized by "non-culturability" and a substantial decrease of metabolic activity and global transcription rates. Here, we found that the transition of from the dormant "non-culturable" (NC) cells to fully replicating population occurred not earlier than 7 days after the start of the resuscitation process, with predominant resuscitation over this time interval evidenced by shortening apparent generation time up to 2.8 h at the beginning of resuscitation. The early resuscitation phase was characterized by constant, albeit low, incorporation of radioactive uracil, indicating transcription immediately after the removal of the stress factor, which resulted in significant changes of the transcriptional profile already after the first 24 h of resuscitation. This early response included transcriptional upregulation of genes encoding enzymes of fatty acid synthase system type I (FASI) and type II (FASII) responsible for fatty acid/mycolic acid biosynthesis, and regulatory genes, including encoding a redox-sensing transcription factor. The second resuscitation phase took place 4 days after the resuscitation onset, i.e., still before the start of active cell division, and included activation of central metabolism genes encoding NADH dehydrogenases, ATP-synthases, and ribosomal proteins. Our results demonstrate, for the first time, that the resuscitation of dormant NC is characterized by immediate activation of transcription followed by the upregulation of genes controlling key metabolic pathways and then, cell multiplication.
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http://dx.doi.org/10.3389/fcimb.2019.00272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6689984PMC
July 2020

Assessment of piRNA biogenesis and function in testicular germ cell tumors and their precursor germ cell neoplasia in situ.

BMC Cancer 2018 01 4;18(1):20. Epub 2018 Jan 4.

Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia, 117997.

Background: Aberrant overexpression of PIWI/piRNA pathway proteins is shown for many types of tumors. Interestingly, these proteins are downregulated in testicular germ cell tumors (TGCTs) compared to normal testis tissues. Here, we used germline and TGCT markers to assess the piRNA biogenesis and function in TGCTs and their precursor germ cell neoplasia in situ (GCNIS).

Methods: We used small RNA deep sequencing, qRT-PCR, and mining public RNAseq/small RNA-seq datasets to examine PIWI/piRNA gene expression and piRNA biogenesis at four stages of TGCT development: (i) germ cells in healthy testis tissues, (ii) germ cells in testis tissues adjacent to TGCTs, (iii) GCNIS cells and (iv) TGCT cells. To this end, we studied three types of samples: (a) healthy testis, (b) testis tissues adjacent to two types of TGCTs (seminomas and nonseminomas) and containing both germ cells and GCNIS cells, as well as (c) matching TGCT samples.

Results: Based on our analyses of small RNA-seq data as well as the presence/absence of expression correlation between PIWI/piRNA pathway genes and germline or TGCT markers, we can suggest that piRNA biogenesis is intact in germ cells present in healthy adult testes, and adjacent to TGCTs. Conversely, GCNIS and TGCT cells were found to lack PIWI/piRNA pathway gene expression and germline-like piRNA biogenesis. However, using an in vitro cell line model, we revealed a possible role for a short PIWIL2/HILI isoform expressed in TGCTs in posttranscriptional regulation of the youngest members of LINE and SINE classes of transposable elements. Importantly, this regulation is also implemented without involvement of germline-like biogenesis of piRNAs.

Conclusions: Though further studies are warranted, these findings suggest that the conventional germline-like PIWI/piRNA pathway is lost in transition from germ cells to GCNIS cells.
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http://dx.doi.org/10.1186/s12885-017-3945-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5755174PMC
January 2018

Two modes of targeting transposable elements by piRNA pathway in human testis.

RNA 2017 11 25;23(11):1614-1625. Epub 2017 Aug 25.

Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.

PIWI proteins and their partner small RNAs, termed piRNAs, are known to control transposable elements (TEs) in the germline. Here, we provide evidence that in humans this control is exerted in two different modes. On the one hand, production of piRNAs specifically targeting evolutionarily youngest TEs (L1HS, L1PA2-L1PA6, LTR12C, SVA) is present both at prenatal and postnatal stages of spermatogenesis and is performed without involvement of piRNA clusters. On the other hand, at postnatal stages, piRNAs deriving from pachytene clusters target "older" TEs and thus complement cluster-independent piRNA production to achieve relevant targeting of virtually all TEs expressed in postnatal testis. We also find that converging transcription of antisense-oriented genes contributes to the origin of genic postnatal prepachytene clusters. Finally, while a fraction of pachytene piRNAs was previously shown to arise from long intergenic noncoding RNAs (lincRNAs, i.e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis.
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http://dx.doi.org/10.1261/rna.060939.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5648030PMC
November 2017

Intragenic Locus in Human PIWIL2 Gene Shares Promoter and Enhancer Functions.

PLoS One 2016 1;11(6):e0156454. Epub 2016 Jun 1.

Department of Genomics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

Recently, more evidence supporting common nature of promoters and enhancers has been accumulated. In this work, we present data on chromatin modifications and non-polyadenylated transcription characteristic for enhancers as well as results of in vitro luciferase reporter assays suggesting that PIWIL2 alternative promoter in exon 7 also functions as an enhancer for gene PHYHIP located 60Kb upstream. This finding of an intragenic enhancer serving as a promoter for a shorter protein isoform implies broader impact on understanding enhancer-promoter networks in regulation of gene expression.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0156454PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4889060PMC
July 2017

Distinguishing epigenetic features of preneoplastic testis tissues adjacent to seminomas and nonseminomas.

Oncotarget 2016 Apr;7(16):22439-47

Department of Genetics and Postgenomic Technologies, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

PIWI pathway proteins are expressed during spermatogenesis where they play a key role in germ cell development. Epigenetic loss of PIWI proteins expression was previously demonstrated in testicular germ cell tumors (TGCTs), implying their involvement in TGCT development. In this work, apart from studying only normal testis and TGCT samples, we also analyzed an intermediate stage, i.e. preneoplastic testis tissues adjacent to TGCTs. Importantly, in this study, we minimized the contribution of patient-to-patient heterogeneity by using matched preneoplastic/TGCT samples. Surprisingly, expression of germ cell marker DDX4 suggests that spermatogenesis is retained in premalignant testis tissues adjacent to nonseminoma, but not those adjacent to seminoma. Moreover, this pattern is followed by expression of PIWI pathway genes, which impacts one of their functions: DNA methylation level over LINE-1 promoters is higher in preneoplastic testis tissues adjacent to nonseminomas than those adjacent to seminomas. This finding might imply distinct routes for development of the two types of TGCTs and could be used as a novel diagnostic marker, possibly, noninvasively. Finally, we studied the role of CpG island methylation in expression of PIWI genes in patient samples and using in vitro experiments in cell line models: a more complex interrelation between DNA methylation and expression of the corresponding genes was revealed.
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http://dx.doi.org/10.18632/oncotarget.7074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008371PMC
April 2016

Brentuximab vedotin in the treatment of a patient with refractory Hodgkin disease and Proteus syndrome - a case report and discussion.

Clin Case Rep 2015 Jul 11;3(7):646-9. Epub 2015 Jun 11.

Federal Center for Pediatric Hematology, Oncology and Immunology, Named by D. Rogachev Moscow, Russia.

Treatment of patients with refractory Hodgkin lymphoma is a significant issue. We report a patient with Proteus syndrome and relapsed Hodgkin lymphoma, whose remission was finally achieved after brentuximab vedotin therapy, allowing her to receive a haploidentical stem cell transplant. The possible relationship between both disorders was discussed.
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http://dx.doi.org/10.1002/ccr3.297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527816PMC
July 2015

Single-Center Experience of Unrelated and Haploidentical Stem Cell Transplantation with TCRαβ and CD19 Depletion in Children with Primary Immunodeficiency Syndromes.

Biol Blood Marrow Transplant 2015 Nov 15;21(11):1955-62. Epub 2015 Jul 15.

Department of Hematopoietic Stem Cell Transplantation, Dmitry Rogachev Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

The transplantation of stem cells from a matched unrelated donor (MUD) or a haploidentical mismatched related donor (MMRD) is a widely used variant of curative treatment for patients with primary immunodeficiency (PID). Currently, different strategies are used to reduce the risk of post-transplant complications and enhance immune reconstitution. We report the preliminary results of MUD and MMRD transplantation with TCRαβ/CD19 depletion in patients with PID (trial registered at www.clinicaltrials.gov as NCT02327351). Thirty-seven PID patients (median age, 2.6 years; range, .2 to 17) were transplanted from MUDs (n = 27) or haploidentical MMRDs (n = 10) after TCRαβ(+)/CD19(+) graft depletion. The median numbers of CD34(+) and TCRαβ(+) cells in the graft were 11.7 × 10(6)/kg and 10.6 × 10(3)/kg, respectively. Acute graft-versus-host disease (GVHD) was observed in 8 patients (22%), without a statistically significant difference between MUDs and MMRDs; 7 of these patients had grade II acute GVHD and responded to first-line therapy, whereas 1 patient had grade IV acute GVHD with transformation to extensive chronic GVHD. Primary and secondary graft failure (nonengraftment or rejection) was observed in 10 patients (27%), 9 of whom were treated with 1 alkylating agent in the conditioning regimen. All these patients were successfully retransplanted with different rescue protocols. Preliminary data on immune reconstitution were very encouraging. Most patients had significant numbers of T lymphocytes detected on the first assessment (day +30) and more than 500 T cells/μL, on day +120. Based on our preliminary data, no significant difference was seen between MMRD and MUD hematopoietic stem cell transplantation (HSCT). With a median follow-up period of 15 months, the cumulative probabilities of overall patient survival and transplant-related mortality were 96.7% and 3.3%, respectively. Based on the results, the ability to control the main post-transplant complications and the immune reconstitution rates are the main factors leading to successful outcome in patients with PID after TCRαβ(+)-depleted HSCT.
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http://dx.doi.org/10.1016/j.bbmt.2015.07.008DOI Listing
November 2015

Expression profiles of PIWIL2 short isoforms differ in testicular germ cell tumors of various differentiation subtypes.

PLoS One 2014 10;9(11):e112528. Epub 2014 Nov 10.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.

PIWI family proteins have recently emerged as essential contributors in numerous biological processes including germ cell development, stem cell maintenance and epigenetic reprogramming. Expression of some of the family members has been shown to be elevated in tumors. In particular, PIWIL2 has been probed as a potential neoplasia biomarker in many cancers in humans. Previously, PIWIL2 was shown to be expressed in most tumours as a set of its shorter isoforms. In this work, we demonstrated the presence of its 60 kDa (PL2L60A) and 80 kDa (PL2L80A) isoforms in testicular cancer cell lines. We also ascertained the transcriptional boundaries of mRNAs and alternative promoter regions for these PIWIL2 isoforms. Further, we probed a range of testicular germ cell tumor (TGCT) samples and found PIWIL2 to be predominantly expressed as PL2L60A in most of them. Importantly, the levels of both PL2L60A mRNA and protein products were found to vary depending on the differentiation subtype of TGCTs, i.e., PL2L60A expression is significantly higher in undifferentiated seminomas and appears to be substantially decreased in mixed and nonseminomatous TGCTs. The higher level of PL2L60A expression in undifferentiated TGCTs was further validated in the model system of retinoic acid induced differentiation in NT2/D1 cell line. Therefore, both PL2L60A mRNA and protein abundance could serve as an additional marker distinguishing between seminomas and nonseminomatous tumors with different prognosis and therapy approaches.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112528PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4226551PMC
December 2015

Recovery of ovarian function and pregnancy in a patient with AML after myeloablative busulphan-based conditioning regimen.

J Pediatr Hematol Oncol 2011 May;33(4):e154-5

Federal Research and Clinical Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

We report a rare case of ovarian function recovery and pregnancy after hormone-replacement therapy (HRT) in the acute myeloblastic leukemia (AML) patient in third complete remission received hematopoietic stem cell transplantation (HSCT) with busulphan-based conditioning regimen. Successful engraftment of the donor cells and full donor's chimerism was achieved without the signs of leukemia. One year after HSCT the patient received a course of HRT as a treatment of hypergonadotropic hypogonadism. After 12 months of HRT the recovery of ovarian function was confirmed. Eight years after the HSCT spontaneous pregnancy occurred; heartbeat of the fetus was registered on week 7. Three weeks later a nonsevere vaginal bleeding occurred and the ultrasound examination showed a nondeveloping pregnancy. Genetic examination of the abortion material showed a full triploid genotype (69 XXX). To our knowledge this is a first case of ovarian function restoration and spontaneous pregnancy in a AML patient after multiple courses of high-dose chemotherapy and busulphan-based myeloablative conditioning for HSCT.
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http://dx.doi.org/10.1097/MPH.0b013e3181faf7b5DOI Listing
May 2011

Tissue phantoms constructed with hydrophobic nanoporous silica particles.

Anal Chem 2010 Aug;82(15):6712-6

Department of Chemistry and the Nanoscience and Nanotechnology Institute, The University of Iowa, Iowa City, Iowa 52242, USA.

We describe a protocol to create tissue phantoms with hydrophobic nanoporous particles. The nanopores of the particles are loaded with biological molecules at the desired compositions. Tissue phantoms are prepared by immersing dried particles into aqueous biological matrixes. The hydrophobicity of the pore surface prevents the solution from penetrating into the nanopores, thus preserving the designed molecular composition inside the particles. This protocol provides a unique approach to preparing biological systems in small domains, at micrometer and nanometer dimensions, with well-defined boundaries and tailored biological and optical properties. The nanoporous particle approach is easy when compared to the common preparation methods such as with polymers and vesicles as it involves direct loading of the biological molecules into the pores and does not require complex synthetic steps. The method is adaptable, with tunable pore and particle sizes, and robust, with a rigid boundary to protect the designed biological domain. In addition to tissue phantom preparation, this approach is applicable in systems where a well-defined biological domain is desired.
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http://dx.doi.org/10.1021/ac902442gDOI Listing
August 2010

Dramatic red-shifted fluorescence of [2.2]paracyclophanes with peripheral substituents attached to the saturated bridges.

Org Lett 2009 Nov;11(22):5106-9

Department of Chemistry and The Optical Science and Technology Center, University of Iowa, Iowa City, Iowa 52242, USA.

A bridge-substituted [2.2]paracyclophane obtained from the organic solid state exhibits a dramatic red shift in fluorescence relative to [2.2]paracyclophane. A further red shift occurs upon alkylation of the pyridylcyclobutyl bridges. Our results demonstrate that [2.2]cyclophanes substituted at the bridge, despite not being attached via the extended pi-system, are promising building blocks in the development of optical materials.
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http://dx.doi.org/10.1021/ol901907jDOI Listing
November 2009

Methylation-free site patterns along a 1-Mb locus on Chr19 in cancerous and normal cells are similar. A new fast approach for analyzing unmethylated CCGG sites distribution.

Mol Genet Genomics 2006 Jun 25;275(6):615-22. Epub 2006 Feb 25.

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 16/10 Miklukho-Maklaya st., 117997, Moscow, Russia.

We describe a newly developed technique for rapid identification of positions of genomic DNA breaks, preexisting or introduced by specific digestion, in particular, by restriction endonucleases (RIDGES). We applied RIDGES in analyzing unmethylated CCGG sites distribution along a 1-Mb long genome region (D19S208-COX7A1 on chromosome 19) in cancerous and normal lung tissues. Both tissues were characterized by a profoundly uneven density of unmethylated sites along the fragment. Interestingly, the distribution of hypomethylated regions did not correlate with gene locations within the fragment, and one of the most hypomethylated areas contained practically no genes. We also demonstrated that the methylation pattern of a long genome DNA fragment was rather stable and practically unchanged in human lung cancer tissue as compared with its normal counterpart, in accordance with the suggestion (Ross et al. in Nat Genet 24:227-235, 2000) that cell lines of common origin have typically similar transcription profiles. An analogous suggestion might probably be made for global methylation patterns of genomic DNA.
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http://dx.doi.org/10.1007/s00438-006-0111-2DOI Listing
June 2006
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