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Yin J, Huang H, Zheng M, Hu J. An ultrasonic biosample disruptor with two triangular teeth on its radiation face. Biotechnol J 2024; 19:e2300263. [PMID: 38009259 DOI: 10.1002/biot.202300263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 11/09/2023] [Accepted: 11/23/2023] [Indexed: 11/28/2023]
Abstract
Ultrasound has been used in biosample disruption such as disruption of algal cell and DNA. New structure of ultrasonic biosample disruptor (UBD) needs to be explored to increase the energy efficiency. In this study, an UBD with two triangular teeth on the bottom radiation face of the water tank has been proposed, to concentrate the acoustic energy into the slot between the two neighboring triangular teeth, in order to raise the acoustic energy utilization and fragmentation performance. The acoustic energy concentration into the slot is verified by the FEM computation, and the improvement of fragmentation performance is experimentally confirmed with spirulina and tribonema, compared to the traditional UBD which has a flat radiation face. The number proportion of fragment in the length range of 10-20 μm generated by the UBD proposed in this work is 17.08% and 10.82% more than that generated by the traditional UBD for the two samples, respectively. Besides, the UBD proposed in this work has a much smaller standard deviation of DNA fragment length (47 bp) than the traditional UBD (249 bp), with a similar mean length of fragments. Moreover, the maximum weight proportion of fragment in the range of 100-300 bp, generated by the UBD proposed in this work, is 71.4%.
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Affiliation(s)
- Jia Yin
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | - Huiyu Huang
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
| | | | - Junhui Hu
- State Key Lab of Mechanics and Control for Aerospace Structures, Nanjing University of Aeronautics and Astronautics, Nanjing, China
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2
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Liu X, Liu H, Wang Y, Li M, Ji L, Wang K, Wei C, Li W, Chen C, Yu L, Zhu X, Hong X. Chromosome-Level Analysis of the Pelochelys cantorii Genome Provides Insights to Its Immunity, Growth and Longevity. BIOLOGY 2023; 12:939. [PMID: 37508370 PMCID: PMC10376104 DOI: 10.3390/biology12070939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The Asian giant soft-shelled turtle, Pelochelys cantorii (Trionychidae), is one of the largest aquatic turtles in China and was designated as a First-Grade Protected Animal in China in 1989. Previous investigation based on a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies acquired a high-quality chromosome-level genome of Pc. cantorii. In this study, comparative genomic analysis between Pc. cantorii and 16 other vertebrate genomes indicated that turtles separated from the ancestor of archosaurians approximately 256.6 (95% highest posterior density interval, 263.6-251.9) million years ago (Mya) (Upper Permian to Triassic) and that Pc. cantorii separated from the ancestor of Pd. sinensis and R. swinhoei approximately 59.3 (95% highest posterior density interval, 64.3-54.3) Mya. Moreover, several candidate genes, such as VWA5A, ABCG2, A2M and IGSF1, associated with tumor suppression, growth and age were expanded, implicating their potential roles in the exceptional longevity of turtles. This new chromosome-level assembly has important scientific value in the study of conservation of Pc. cantorii and also enriches the evolutionary investigation of turtle species.
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Affiliation(s)
- Xiaoli Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Haiyang Liu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Mingzhi Li
- Guangzhou Bio & Data Technology Co., Ltd., Guangzhou 510555, China
| | - Liqin Ji
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Kaikuo Wang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Chengqing Wei
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wei Li
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Chen Chen
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xinping Zhu
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Life Science and Fisheries, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
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Li GB, Pollard J, Liu R, Stevens RC, Quiroz J, Nelson MC, Manahan M, Murgolo N, Ehrick RS, Wallenstein EJ, Hughes J, Tsao YS, Zhao J, Du Z, Tugcu N, Pollard D. Retrospective assessment of clonality of a legacy cell line by analytical subcloning of the master cell bank. Biotechnol Prog 2021; 38:e3215. [PMID: 34586757 DOI: 10.1002/btpr.3215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/06/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022]
Abstract
In recent years, assurance of clonality of the production cell line has been emphasized by health authorities during review of regulatory submissions. When insufficient assurance of clonality is provided, augmented control strategies may be required for a commercial production process. In this study, we conducted a retrospective assessment of clonality of a legacy cell line through analysis of subclones from the master cell bank (MCB). Twenty-four subclones were randomly selected based on a predetermined acceptance sampling plan. All these subclones share a conserved integration junction, thus providing a high level of assurance that the cell population in the MCB was derived from a single progenitor cell. However, Southern blot analysis indicates that at least four subpopulations possibly exist in the MCB. Additional characterization of these four subpopulations demonstrated that the resulting changes in product quality attributes of some subclones are not related to the genetic heterogeneity observed in Southern blot hybridization. Furthermore, process consistency, process comparability, and analytical comparability have been demonstrated in batches produced across varying manufacturing processes, scales, facilities, cell banks, and cell ages. Finally, process and product consistency together with a high level of assurance of clonal origin of the MCB helped clear the hurdle for regulatory approval without requirement of additional control strategies.
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Affiliation(s)
- Guanghua Benson Li
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jennifer Pollard
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Ren Liu
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Richard C Stevens
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jorge Quiroz
- Research CMC Statistics, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Michael C Nelson
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Matthew Manahan
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Nicholas Murgolo
- Genetics and Pharmacogenomics, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Robin S Ehrick
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Eric J Wallenstein
- Biologics Process Development & Commercialization, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jason Hughes
- Global Research IT, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Yung-Shyeng Tsao
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Jia Zhao
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Zhimei Du
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - Nihal Tugcu
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
| | - David Pollard
- Biologics Process Research & Development, Merck & Co., Inc., Kenilworth, New Jersey, USA
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Lee Z, Raabe M, Hu WS. Epigenomic features revealed by ATAC-seq impact transgene expression in CHO cells. Biotechnol Bioeng 2021; 118:1851-1861. [PMID: 33521928 DOI: 10.1002/bit.27701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 12/15/2022]
Abstract
Different regions of a mammalian genome have different accessibilities to transcriptional machinery. The integration site of a transgene affects how actively it is transcribed. Highly accessible genomic regions called super-enhancers have been recently described as strong regulatory elements that shape cell identity. Super-enhancers have been identified in Chinese hamster ovary (CHO) cells using the Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq). Genes near super-enhancer regions had high transcript levels and were enriched for oncogenic signaling and proliferation functions, consistent with an immortalized phenotype. Inaccessible regions in the genome with low ATAC signal also had low transcriptional activity. Genes in inaccessible regions were enriched for remote tissue functions such as taste, smell, and neuronal activation. A lentiviral reporter integration assay showed integration into super-enhancer regions conferred higher reporter expression than insertion into inaccessible regions. Targeted integration of an IgG vector into the Plec super-enhancer region yielded clones that expressed the immunoglobulin light chain gene mostly in the top 20% of all transcripts with the majority in the top 5%. The results suggest the epigenomic landscape of CHO cells can guide the selection of integration sites in the development of cell lines for therapeutic protein production.
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Affiliation(s)
- Zion Lee
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Marina Raabe
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
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Slesarev A, Viswanathan L, Tang Y, Borgschulte T, Achtien K, Razafsky D, Onions D, Chang A, Cote C. CRISPR/CAS9 targeted CAPTURE of mammalian genomic regions for characterization by NGS. Sci Rep 2019; 9:3587. [PMID: 30837529 PMCID: PMC6401131 DOI: 10.1038/s41598-019-39667-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 01/30/2019] [Indexed: 01/08/2023] Open
Abstract
The robust detection of structural variants in mammalian genomes remains a challenge. It is particularly difficult in the case of genetically unstable Chinese hamster ovary (CHO) cell lines with only draft genome assemblies available. We explore the potential of the CRISPR/Cas9 system for the targeted capture of genomic loci containing integrated vectors in CHO-K1-based cell lines followed by next generation sequencing (NGS), and compare it to popular target-enrichment sequencing methods and to whole genome sequencing (WGS). Three different CRISPR/Cas9-based techniques were evaluated; all of them allow for amplification-free enrichment of target genomic regions in the range from 5 to 60 fold, and for recovery of ~15 kb-long sequences with no sequencing artifacts introduced. The utility of these protocols has been proven by the identification of transgene integration sites and flanking sequences in three CHO cell lines. The long enriched fragments helped to identify Escherichia coli genome sequences co-integrated with vectors, and were further characterized by Whole Genome Sequencing (WGS). Other advantages of CRISPR/Cas9-based methods are the ease of bioinformatics analysis, potential for multiplexing, and the production of long target templates for real-time sequencing.
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Affiliation(s)
- Alexei Slesarev
- BioReliance Corp., 14920 Broschart Road, Rockville, MD, 20850, USA.
| | | | - Yitao Tang
- BioReliance Corp., 14920 Broschart Road, Rockville, MD, 20850, USA
| | | | | | - David Razafsky
- MilliporeSigma, 2909 Laclede Avenue, Saint Louis, MO, 63103, USA
| | - David Onions
- BioReliance Corp., 14920 Broschart Road, Rockville, MD, 20850, USA
| | - Audrey Chang
- BioReliance Corp., 14920 Broschart Road, Rockville, MD, 20850, USA
| | - Colette Cote
- BioReliance Corp., 14920 Broschart Road, Rockville, MD, 20850, USA
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Bandyopadhyay AA, O’Brien SA, Zhao L, Fu HY, Vishwanathan N, Hu WS. Recurring genomic structural variation leads to clonal instability and loss of productivity. Biotechnol Bioeng 2019; 116:41-53. [PMID: 30144379 PMCID: PMC7058117 DOI: 10.1002/bit.26823] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/13/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022]
Abstract
Chinese hamster ovary cells, commonly used in the production of therapeutic proteins, are aneuploid. Their chromosomes bear structural abnormality and undergo changes in structure and number during cell proliferation. Some production cell lines are unstable and lose their productivity over time in the manufacturing process and during the product's life cycle. To better understand the link between genomic structural changes and productivity stability, an immunoglobulin G producing cell line was successively single-cell cloned to obtain subclones that retained or lost productivity, and their genomic features were compared. Although each subclone started with a single karyotype, the progeny quickly diversified to a population with a distribution of chromosome numbers that is not distinctive from the parent and among subclones. The comparative genomic hybridization (CGH) analysis showed that the extent of copy variation of gene coding regions among different subclones stayed at levels of a few percent. Genome regions that were prone to loss of copies, including one with a product transgene integration site, were identified in CGH. The loss of the transgene copy was accompanied by loss of transgene transcript level. Sequence analysis of the host cell and parental producing cell showed prominent structural variations within the regions prone to loss of copies. Taken together, we demonstrated the transient nature of clonal homogeneity in cell line development and the retention of a population distribution of chromosome numbers; we further demonstrated that structural variation in the transgene integration region caused cell line instability. Future cell line development may target the transgene into structurally stable regions.
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Affiliation(s)
| | | | | | | | | | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455-0132 USA
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Genome sequence comparison between Chinese hamster ovary (CHO) DG44 cells and mouse using end sequences of CHO BAC clones based on BAC-FISH results. Cytotechnology 2018; 70:1399-1407. [PMID: 29987698 DOI: 10.1007/s10616-018-0233-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/16/2018] [Indexed: 11/26/2022] Open
Abstract
Chinese hamster ovary (CHO) cells have frequently been used in biotechnology as a mammalian host cell platform for expressing genes of interest. Previously, we constructed a detailed physical chromosomal map of the CHO DG44 cell line by fluorescence in situ hybridization (FISH) imaging using 303 bacterial artificial chromosome (BAC) clones as hybridization probes (BAC-FISH). BAC-FISH results revealed that the two longest chromosomes were completely paired. However, other chromosomes featured partial deletions or rearrangements. In this study, we determined the end sequences of 303 BAC clones (BAC end sequences), which were used for BAC-FISH probes. Among 606 BAC-end sequences (BESs) (forward and reverse ends), 558 could be determined. We performed a comparison between all determined BESs and mouse genome sequences using NCBI BLAST. Among these 558 BESs, 465 showed high homology to mouse chromosomal sequences. We analyzed the locations of these BACs in chromosomes of the CHO DG44 cell line using a physical chromosomal map. From the obtained results, we investigated the regional similarities among CHO chromosomes (A-T) and mouse chromosomes (1-19 and sex) about 217 BESs (46.7% of 465 high homologous BESs). Twenty-three specific narrow regions in 13 chromosomes of the CHO DG44 cell line showed high homology to mouse chromosomes, but most of other regions did not show significant correlations with the mouse genome. These results contribute to accurate alignments of chromosomes of Chinese hamster and its genome sequence, analysis of chromosomal instability in CHO cells, and the development of target locations for gene and/or genome editing techniques.
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Richelle A, Lewis NE. Improvements in protein production in mammalian cells from targeted metabolic engineering. ACTA ACUST UNITED AC 2017; 6:1-6. [PMID: 29104947 DOI: 10.1016/j.coisb.2017.05.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bioprocess optimization has yielded powerful clones for biotherapeutic production. However, new genomic technologies allow more targeted approaches to cell line development. Here we review efforts to enhance protein production in mammalian cells through metabolic engineering. Most efforts aimed to reduce toxic byproducts accumulation to enhance protein productivity. However, recent work highlights the possibility of regulating other desirable traits (e.g., apoptosis and glycosylation) by targeting central metabolism since these processes are interconnected. Therefore, as we further detail the pathways underlying cell growth and protein production and deploy diverse algorithms for their analysis, opportunities will arise to move beyond simple cell line designs and facilitate cell engineering strategies with complex combinations of genes that together underlie a phenotype of interest.
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Affiliation(s)
- Anne Richelle
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.,Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States
| | - Nathan E Lewis
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States.,Department of Pediatrics, University of California, San Diego, School of Medicine, La Jolla, CA 92093, United States
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Vishwanathan N, Bandyopadhyay A, Fu HY, Johnson KC, Springer NM, Hu WS. A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines. Biotechnol Bioeng 2017; 114:1903-1908. [DOI: 10.1002/bit.26311] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/28/2017] [Accepted: 04/09/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Nandita Vishwanathan
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Arpan Bandyopadhyay
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Hsu-Yuan Fu
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Kathryn C. Johnson
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
| | - Nathan M. Springer
- Microbial and Plant Genomics Institute and Department of Plant Biology; University of Minnesota; St. Paul Minnesota
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science; University of Minnesota; 421 Washington Avenue SE Minneapolis Minnesota 55455-0132
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