20,717 results match your criteria rna repeat


The potential roles of different metacaspases in maize defense response.

Plant Signal Behav 2021 Apr 12:1906574. Epub 2021 Apr 12.

The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, PR China.

Metacaspases (MCs), a class of cysteine-dependent proteases, act as important regulators in plant defense response. In maize genome, there are 11 which have been categorized into two types (type I and II) based on their structural differences. In this study, we investigated the different transcript patterns of 11 in maize defense response mediated by the nucleotide-binding, leucine-rich-repeat protein Rp1-D21. Read More

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Telomeric Double Strand Breaks in G1 Human Cells Facilitate Formation of 5' C-Rich Overhangs and Recruitment of TERRA.

Front Genet 2021 25;12:644803. Epub 2021 Mar 25.

Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, United States.

Telomeres, repetitive nucleoprotein complexes that protect chromosomal termini and prevent them from activating inappropriate DNA damage responses (DDRs), shorten with cell division and thus with aging. Here, we characterized the human cellular response to targeted telomeric double-strand breaks (DSBs) in telomerase-positive and telomerase-independent alternative lengthening of telomere (ALT) cells, specifically in G1 phase. Telomeric DSBs in human G1 cells elicited early signatures of a DDR; however, localization of 53BP1, an important regulator of resection at broken ends, was not observed at telomeric break sites. Read More

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Novel Variant Linked to Amyotrophic Lateral Sclerosis Risk and Clinical Phenotype.

Front Aging Neurosci 2021 26;13:658226. Epub 2021 Mar 26.

Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia.

Objective: There is a critical need to establish genetic markers that explain the complex phenotypes and pathogenicity of ALS. This study identified a polymorphism in the Stathmin-2 gene and investigated its association with sporadic ALS (sALS) disease risk, age-of onset and survival duration.

Methods: The candidate CA repeat was systematically analyzed using PCR, Sanger sequencing and high throughput capillary separation for genotyping. Read More

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Gene Therapy for ALS: A Review.

Mol Ther 2021 Apr 8. Epub 2021 Apr 8.

Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA USA 19104; Children's Hospital of Philadelphia, Philadelphia, PA USA 19104. Electronic address:

Amyotrophic lateral sclerosis (ALS) has historically posed unique challenges for gene therapy-based approaches, due to a paucity of therapeutic targets as well as the difficulty of accessing both the brain and spinal cord. Recent advances in our understanding of disease mechanism and ALS genetics, however, have combined with tremendous strides in CNS targeting, gene delivery, and gene editing and knockdown techniques to open new horizons of therapeutic possibility. Gene therapy clinical trials are currently underway for ALS patients with SOD1 mutations, C9orf72 hexanucleotide repeat expansions, ATXN2 trinucleotide expansions, and FUS mutations, as well as sporadic disease without known genetic cause. Read More

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Targeting the ALS/FTD-associated A-DNA kink with anthracene-based metal complex causes DNA backbone straightening and groove contraction.

Nucleic Acids Res 2021 Apr 9. Epub 2021 Apr 9.

Department of Life Sciences, National Chung-Hsing University, Taichung 402, Taiwan.

The use of a small molecule compound to reduce toxic repeat RNA transcripts or their translated aberrant proteins to target repeat-expanded RNA/DNA with a G4C2 motif is a promising strategy to treat C9orf72-linked disorders. In this study, the crystal structures of DNA and RNA-DNA hybrid duplexes with the -GGGCCG- region as a G4C2 repeat motif were solved. Unusual groove widening and sharper bending of the G4C2 DNA duplex A-DNA conformation with B-form characteristics inside was observed. Read More

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Hypothesis and Theory: Roles of Arginine Methylation in C9orf72-Mediated ALS and FTD.

Front Cell Neurosci 2021 23;15:633668. Epub 2021 Mar 23.

ALS Therapy Development Institute, Cambridge, MA, United States.

Hexanucleotide repeat expansion (G4C2) mutations in the gene C9ORF72 account for approximately 30% of familial cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as well as approximately 7% of sporadic cases of ALS. G4C2 mutations are known to result in the production of five species of dipeptide repeat proteins (DRPs) through non-canonical translation processes. Arginine-enriched dipeptide repeat proteins, glycine-arginine (polyGR), and proline-arginine (polyPR) have been demonstrated to be cytotoxic and deleterious in multiple experimental systems. Read More

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CircANKRD11 Knockdown Protects HPMECs from Cigarette Smoke Extract-Induced Injury by Regulating miR-145-5p/BRD4 Axis.

Int J Chron Obstruct Pulmon Dis 2021 1;16:887-899. Epub 2021 Apr 1.

Department of Physical Examination Center, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, People's Republic of China.

Background: Chronic obstructive pulmonary disease (COPD) is a major cause of death because of its high incidence and mortality, which is chiefly resulted from cigarette smoke exposure. A large number of studies show that circular RNA (circRNA) participates in regulating COPD process. This study aims to reveal the role of circRNA ankyrin repeat domain 11 (circANKRD11) in cigarette smoke extract (CSE)-induced cell apoptosis, inflammation, and oxidative stress. Read More

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Etravirine in treatment-experienced HIV-1 infected children 1-<6 years of age.

AIDS 2021 Apr 6. Epub 2021 Apr 6.

University of Colorado Anschutz Medical Campus, Aurora, CO Children's Hospital of Philadelphia, Philadelphia, PA Jacobi Medical Center, Albert Einstein College of Medicine, Bronx, NY Frontier Science and Technology, Buffalo, NY Harvard School of Public Health, Boston, MA Shandukani Research Centre, Johannesburg, South Africa FHI 360, Durham, NC ColumbusUSA Technologies contract at NIAID, Maternal, Adolescent & Pediatric Research Branch, Rockville, MD Eunice Kennedy Shriver National Institute of Child Health & Human Development, Bethesda, MD IMPAACT Laboratory Center, University of California Los Angeles, Los Angeles, CA Preventive Medicine Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil Janssen, Research and Development, Beerse, Belgium.

Objective: To describe the pharmacokinetics (PK), safety, and efficacy of etravirine (ETR) in HIV-infected children 1 to < 6 yrs.

Design: Phase I/II, open label, multicenter, dose-finding study.

Methods: Antiretroviral (ARV)-experienced children in two age cohorts (I: 2-<6 yr; II: 1-<2 yr) received weight-based ETR, swallowed whole or dispersed in liquid, with optimized ARV therapy including a ritonavir-boosted protease inhibitor. Read More

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Chemical Modification and Transformation Strategies of Guide RNAs in CRISPR-Cas9 Gene Editing Systems.

Chempluschem 2021 Mar 18;86(4):587-600. Epub 2021 Mar 18.

State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China.

The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated protein 9) is a most powerful tool and has been widely used in gene editing and gene regulation since its discovery. However, wild-type CRISPR-Cas9 suffers from off-target effects and low editing efficiency. To overcome these limitations, engineered Cas9 proteins have been extensively investigated. Read More

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Complete chloroplast genome and phylogenetic analysis of a wild grass, Bowden.

Mitochondrial DNA B Resour 2021 Mar 26;6(3):1219-1221. Epub 2021 Mar 26.

State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, PR China.

The complete circular chloroplast (cp) genome of wild Bowden was sequenced and reported in this study. The complete chloroplast genome of wild was 12,753 bp in length, including a pair of inverted repeat regions (IRA/IRB) of 21,587 bp separated by one small single-copy (SSC) region of 12,753 bp and one large single-copy (LSC) region of 81,138 bp. A total of 133 genes, including 85 protein-coding genes (PCGs), 40 transfer RNA genes, and 8 ribosomal RNA genes were predicted from the cp genomes. Read More

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Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast.

PLoS Genet 2021 Apr 7;17(4):e1009520. Epub 2021 Apr 7.

Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain.

The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. Read More

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Engineering Protease-Resistant Peptides to Inhibit Human Parainfluenza Viral Respiratory Infection.

J Am Chem Soc 2021 Apr 7. Epub 2021 Apr 7.

Department of Pediatrics, Columbia University Vagelos College of Physicians & Surgeons, New York, New York 10032, United States.

The lower respiratory tract infections affecting children worldwide are in large part caused by the parainfluenza viruses (HPIVs), particularly HPIV3, along with human metapneumovirus and respiratory syncytial virus, enveloped negative-strand RNA viruses. There are no vaccines for these important human pathogens, and existing treatments have limited or no efficacy. Infection by HPIV is initiated by viral glycoprotein-mediated fusion between viral and host cell membranes. Read More

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FOXO1 controls protein synthesis and transcript abundance of mutant polyglutamine proteins, preventing protein aggregation.

Hum Mol Genet 2021 Apr 2. Epub 2021 Apr 2.

University Medical Center Groningen, University of Groningen, Department of Biomedical Sciences of Cells and Systems, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.

FOXO1, a transcription factor downstream of the insulin/insulin like growth factor axis has been linked to protein degradation. Elevated expression of FOXO orthologs can also prevent aggregation of CAG-repeat disease causing polyglutamine (polyQ) proteins but whether FOXO1 targets mutant proteins for degradation is unclear. Here we show that increased expression of FOXO1 prevents toxic polyQ aggregation in human cells while reducing FOXO1 levels has the opposite effect and accelerates it. Read More

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Establishment and characterization of 38 novel patient-derived primary cancer cell lines using multi-region sampling revealing intra-tumor heterogeneity of gallbladder carcinoma.

Hum Cell 2021 Apr 4. Epub 2021 Apr 4.

Department of Biliary I, Shanghai Eastern Hepatobiliary Surgery Hospital, Navy Military Medical University, Shanghai, 200438, China.

Gallbladder carcinoma (GBC) is a lethal biliary tract malignant neoplasm. Patient-derived primary cancer cell lines (PDPCs) are appropriate models to explore biological characteristics and potential therapeutics; however, there is a lack of PDPCs in GBC. In this study, we aimed to establish and characterize the GBC PDPCs, and further investigated the intra-tumor heterogeneity (ITH). Read More

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Tah1, a key component of R2TP complex that regulates assembly of snoRNP, is involved in de novo generation and maintenance of yeast prion [URE3].

J Mol Biol 2021 Mar 31:166976. Epub 2021 Mar 31.

Council of Scientific and Industrial Research-Institute of Microbial Technology, India; Academy of Scientific & Innovative Research, India. Electronic address:

The cellular chaperone machinery plays key role in the de novo formation and propagation of yeast prions (infectious protein). Though the role of Hsp70s in the prion maintenance is well studied, how Hsp90 chaperone machinery affects yeast prions remains unclear. In the current study, we examined the role of Hsp90 and its co-chaperones on yeast prions [PSI] and [URE3]. Read More

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Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in .

Cells 2021 Mar 12;10(3). Epub 2021 Mar 12.

Area of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi City, Ishikawa 923-1292, Japan.

Cytosine-to-Uridine (C-to-U) RNA editing involves the deamination phenomenon, which is observed in animal nucleus and plant organelles; however, it has been considered the U-to-C is confined to the organelles of limited non-angiosperm plant species. Although previous RNA-seq-based analysis implied U-to-C RNA editing events in plant nuclear genes, it has not been broadly accepted due to inadequate confirmatory analyses. Here we examined the U-to-C RNA editing in Arabidopsis tissues at different developmental stages of growth. Read More

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Single-Molecule Long-Read Sequencing of Purslane () and Differential Gene Expression Related with Biosynthesis of Unsaturated Fatty Acids.

Plants (Basel) 2021 Mar 30;10(4). Epub 2021 Mar 30.

School of Design, Shanghai Jiao Tong University, Shanghai 200240, China.

This study aimed to obtain the full-length transcriptome of purslane (); assorted plant samples were used for single-molecule real-time (SMRT) sequencing. Based on SMRT, functional annotation of transcripts, transcript factors (TFs) analysis, simple sequence repeat analysis and long non-coding RNAs (LncRNAs) prediction were accomplished. Total 15. Read More

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Characterization and Vector Competence Studies of Chikungunya Virus Lacking Repetitive Motifs in the 3' Untranslated Region of the Genome.

Viruses 2021 Mar 4;13(3). Epub 2021 Mar 4.

Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany.

Using reverse genetics, we analyzed a chikungunya virus (CHIKV) isolate of the Indian Ocean lineage lacking direct repeat (DR) elements in the 3' untranslated region, namely DR1a and DR2a. While this deletion mutant CHIKV-∆DR exhibited growth characteristics comparable to the wild-type virus in Baby Hamster Kidney cells, replication of the mutant was reduced in C6/36 and Aag2 cells. Using oral and intrathoracic infection of mosquitoes, viral infectivity, dissemination, and transmission of CHIKV-∆DR could be shown for the well-known CHIKV vectors and . Read More

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TERRA: A Novel Biomarker of Embryo Quality and Art Outcome.

Genes (Basel) 2021 Mar 25;12(4). Epub 2021 Mar 25.

Department of Clinical and Experimental Sciences, Unit of Endocrinology and Metabolism, University of Brescia and ASST Spedali Civili Brescia, 25121 Brescia, Italy.

Telomeres are considered to be an internal biological clock, and their progressive shortening has been associated with the risk of age-related diseases and reproductive alterations. Over recent years, an increasing number of studies have focused on the association between telomere length and fertility, identifying sperm telomere length (STL) as a novel biomarker of male fertility. Although typically considered to be repeated DNA sequences, telomeres have recently been shown to also include a long non-coding RNA (lncRNA) known as TERRA (telomeric repeat-containing RNAs). Read More

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Cytological Observation and Transcriptome Comparative Analysis of Self-Pollination and Cross-Pollination in .

Genes (Basel) 2021 Mar 17;12(3). Epub 2021 Mar 17.

College of Life Sciences, Jiangxi Normal University, No 99, Zi Yang Road, Nanchang 330000, China.

is a rare and traditional medicinal plant with high pharmacological and nutritional value. The self-incompatibility mechanism of reproductive isolation was formed in the long-term evolution process, but intraspecific hybridization of different germplasm resources leads to a large gap in the yield, quality, and medicinal value of . To investigate the biological mechanism of self-incompatibility in , cytological observation and the transcriptome analysis was carried out on the samples of self-pollination and cross-pollination in . Read More

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Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor.

PLoS Comput Biol 2021 Apr 2;17(4):e1008890. Epub 2021 Apr 2.

Program in Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, United States of America.

Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. Read More

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Characterization of the complete chloroplast genome sequence of .

Mitochondrial DNA B Resour 2021 Mar 19;6(3):1129-1130. Epub 2021 Mar 19.

Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, China.

The whole complete chloroplast (cp) genome sequence of (formerly ) was sequenced and assembled from Illumina paired-end sequencing. The cp genome of was 157,425 bp long, containing a large single copy region (LSC) of 88,498 bp and a small single copy region (SSC) of 20,475 bp and a pair of inverted repeat regions (IR) of 242,266 bp. It contained 113 different genes, including 79 protein-coding genes, 30 tRNA genes, 4 ribosomal RNA genes. Read More

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The linear mitochondrial genome of commensal hydroid (, , ).

Mitochondrial DNA B Resour 2021 Mar 19;6(3):1082-1084. Epub 2021 Mar 19.

Department of Marine Science, College of Natural Sciences, Incheon National University, Incheon, South Korea.

Here, we present the whole mitochondrial genome of commensal hydroid McCrady 1859 (family Eirinidae); this is the first specimen of the family to have its mitogenome sequenced. The linear mitogenome is 15,315 bp in length and consists of 13 protein-coding genes (PCGs), large and small ribosomal subunits (rRNA), methionine and tryptophan transfer RNA () genes (trnM and trnW), and a partial copy of cytochrome oxidase subunit I () pseudogene, as is typical for the class Hydrozoa. Nucleotide sequences of two genes at two ends of the linear mitogenome form a part of inverted terminal repeat. Read More

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The complete chloroplast genome sequence of coastal psammophyte (Asteraceae, subtribe Crepidinae), in Korea.

Mitochondrial DNA B Resour 2021 Mar 19;6(3):1050-1052. Epub 2021 Mar 19.

Research Institute for Dok-do and Ulleung-do Island, Daegu, Republic of Korea.

We report the first complete chloroplast genome sequence of psammophyte, , on the coastal dunes in Korea. The complete plastid genome is 153,017 bp in total length, with one large single copy (LSC; 84,242 bp), one small single copy (SSC; 18,495 bp), and two inverted repeat (IR) regions (IR and IR, each with 25,140 bp). The overall GC content is 37. Read More

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The complete chloroplast genome sequence of a narrow alpine endemic (Asteraceae), on Jeju Island, Korea.

Mitochondrial DNA B Resour 2021 Mar 18;6(3):1036-1038. Epub 2021 Mar 18.

Research Institute for Dok-do and Ulleung-do Island, Kyungpook National University, Daegu, Republic of Korea.

The first complete chloroplast genome sequence of Jeju Island endemic diploid dandelion, , is reported in this study. The plastome size is 151,554 bp in total length, with one large single copy (LSC; 84,066 bp), one small single copy (SSC; 18,524 bp), and two inverted repeat (IR) regions (IR and IR, each with 24,482 bp). The overall GC content is 37. Read More

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Characterization and phylogenetic analysis of the complete plastome of (Convolvulaceae), an edible vegetable.

Mitochondrial DNA B Resour 2021 Mar 18;6(3):990-992. Epub 2021 Mar 18.

Key Lab of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.

, commonly known as water spinach, is an edible annual vegetable in the genus ,. In this study, the complete plastome of was determined using the Illumina sequencing platform. The plastome size was 162,663 bp. Read More

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The complete chloroplast genome of var. nepalensis (D. Don) Nakai.

Mitochondrial DNA B Resour 2021 Mar 16;6(3):938-940. Epub 2021 Mar 16.

College of Horticulture, Xinyang Agriculture and Forestry University, Xinyang, Henan, China.

var. nepalensis (D. Don) Nakai is an herbaceous species of Rosaceae distributed in China. Read More

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Mitochondrial genome of Glover cucumber biotype (Hemiptera: Aphididae).

Mitochondrial DNA B Resour 2021 Mar 16;6(3):922-924. Epub 2021 Mar 16.

Institute of Cotton Research of Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, Henan, China.

The complete mitochondrial genome of Glover cucumber biotype was sequenced using traditional PCR amplification coupled with Sanger sequencing. The genome is 15,870 bp long, with 83.7% AT content (MW048625). Read More

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Gibberellin signaling mediates lateral root inhibition in response to K+-deprivation.

Plant Physiol 2021 Jan 6. Epub 2021 Jan 6.

Department of Biosciences, Durham University, Durham DH1 3LE, UK.

The potassium ion (K+) is vital for plant growth and development, and K+-deprivation leads to reduced crop yields. Here we describe phenotypic, transcriptomic, and mutant analyses to investigate the signaling mechanisms mediating root architectural changes in Arabidopsis (Arabidopsis thaliana) Columbia. We showed effects on root architecture are mediated through a reduction in cell division in the lateral root (LR) meristems, the rate of LR initiation is reduced but LR density is unaffected, and primary root growth is reduced only slightly. Read More

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January 2021

Coriander Genomics Database: a genomic, transcriptomic, and metabolic database for coriander.

Hortic Res 2020 Apr 1;7(1):55. Epub 2020 Apr 1.

Center for Genomics and Biocomputing/College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063210, China.

Coriander (Coriandrum sativum L.), also known as cilantro, is a globally important vegetable and spice crop. Its genome and that of carrot are models for studying the evolution of the Apiaceae family. Read More

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