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Sanden A, Haas S, Hubbuch J. Modifying an ÄKTApurifier System for the Automated Acquisition of Samples for Kinetic Modeling of Batch Reactions. SLAS Technol 2019; 25:106-110. [PMID: 31829076 DOI: 10.1177/2472630319891976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recording the data necessary to assess the kinetics of a reaction can be labor-intensive. In this technology brief, we show a method to automate this task by utilizing parts of an ÄKTApurifier chromatography system to automatically take samples from a reaction vessel at predefined time intervals and place them in 96-well plates and also enable correlating the samples with in-line spectral data of the reaction solution. Automatic sampling can reduce experimental bottlenecks by enabling overnight reactions or a higher degree of parallelization. To demonstrate the feasibility of the method, we performed batch-PEGylation of lysozyme with varying conditions by changing the molar excess of the PEG reagent. We used analytical cation-exchange chromatography to analyze the samples taken during the batch reaction, determining the concentrations of the individual species present at each time step. Subsequently, we fitted a kinetic model on these data. Fitting the model to four different reaction conditions simultaneously yielded a regression coefficient of R2 = 0.871.
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Affiliation(s)
- Adrian Sanden
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sandra Haas
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jürgen Hubbuch
- Institute of Engineering in Life Sciences, Section IV: Biomolecular Separation Engineering, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Larroude M, Rossignol T, Nicaud JM, Ledesma-Amaro R. Synthetic biology tools for engineering Yarrowia lipolytica. Biotechnol Adv 2018; 36:2150-2164. [PMID: 30315870 PMCID: PMC6261845 DOI: 10.1016/j.biotechadv.2018.10.004] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 09/11/2018] [Accepted: 10/07/2018] [Indexed: 12/15/2022]
Abstract
The non-conventional oleaginous yeast Yarrowia lipolytica shows great industrial promise. It naturally produces certain compounds of interest but can also artificially generate non-native metabolites, thanks to an engineering process made possible by the significant expansion of a dedicated genetic toolbox. In this review, we present recently developed synthetic biology tools that facilitate the manipulation of Y. lipolytica, including 1) DNA assembly techniques, 2) DNA parts for constructing expression cassettes, 3) genome-editing techniques, and 4) computational tools.
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Affiliation(s)
- M Larroude
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - T Rossignol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - J-M Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - R Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, United Kingdom.
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Combinatorial Engineering of Yarrowia lipolytica as a Promising Cell Biorefinery Platform for the de novo Production of Multi-Purpose Long Chain Dicarboxylic Acids. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3030040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Efficient resolution of profen ethyl ester racemates by engineered Yarrowia lipolytica Lip2p lipase. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.tetasy.2017.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Gérard D, Currie F, Medina Gonzalez Y, Camy S, Marty A, Condoret JS. Resolution of 2-bromo-arylacetic acid ester by Yarrowia lipolytica lipase in water/supercritical CO2 two-phase systems. J Supercrit Fluids 2017. [DOI: 10.1016/j.supflu.2016.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Beneyton T, Thomas S, Griffiths AD, Nicaud JM, Drevelle A, Rossignol T. Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica. Microb Cell Fact 2017; 16:18. [PMID: 28143479 PMCID: PMC5282883 DOI: 10.1186/s12934-017-0629-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Droplet-based microfluidics is becoming an increasingly attractive alternative to microtiter plate techniques for enzymatic high-throughput screening (HTS), especially for exploring large diversities with lower time and cost footprint. In this case, the assayed enzyme has to be accessible to the substrate within the water-in-oil droplet by being ideally extracellular or displayed at the cell surface. However, most of the enzymes screened to date are expressed within the cytoplasm of Escherichia coli cells, which means that a lysis step must take place inside the droplets for enzyme activity to be assayed. Here, we take advantage of the excellent secretion abilities of the yeast Yarrowia lipolytica to describe a highly efficient expression system particularly suitable for the droplet-based microfluidic HTS. RESULTS Five hydrolytic genes from Aspergillus niger genome were chosen and the corresponding five Yarrowia lipolytica producing strains were constructed. Each enzyme (endo-β-1,4-xylanase B and C; 1,4-β-cellobiohydrolase A; endoglucanase A; aspartic protease) was successfully overexpressed and secreted in an active form in the crude supernatant. A droplet-based microfluidic HTS system was developed to (a) encapsulate single yeast cells; (b) grow yeast in droplets; (c) inject the relevant enzymatic substrate; (d) incubate droplets on chip; (e) detect enzymatic activity; and (f) sort droplets based on enzymatic activity. Combining this integrated microfluidic platform with gene expression in Y. lipolytica results in remarkably low variability in the enzymatic activity at the single cell level within a given monoclonal population (<5%). Xylanase, cellobiohydrolase and protease activities were successfully assayed using this system. We then used the system to screen for thermostable variants of endo-β-1,4-xylanase C in error-prone PCR libraries. Variants displaying higher thermostable xylanase activities compared to the wild-type were isolated (up to 4.7-fold improvement). CONCLUSIONS Yarrowia lipolytica was used to express fungal genes encoding hydrolytic enzymes of interest. We developed a successful droplet-based microfluidic platform for the high-throughput screening (105 strains/h) of Y. lipolytica based on enzyme secretion and activity. This approach provides highly efficient tools for the HTS of recombinant enzymatic activities. This should be extremely useful for discovering new biocatalysts via directed evolution or protein engineering approaches and should lead to major advances in microbial cell factory development.
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Affiliation(s)
- Thomas Beneyton
- Ecole Supérieure de Physique et de Chimie industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 rue Vauquelin, 75005 Paris, France
- CNRS, University of Bordeaux, CRPP, UPR 8641, 115 Avenue Albert Schweitzer, 33600 Pessac, France
| | - Stéphane Thomas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Andrew D. Griffiths
- Ecole Supérieure de Physique et de Chimie industrielles de la Ville de Paris (ESPCI Paris), CNRS UMR 8231, 10 rue Vauquelin, 75005 Paris, France
| | - Jean-Marc Nicaud
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Antoine Drevelle
- Ets J. Soufflet/CRIS-OSIRIS, Quai Sarrail, BP12, 10400 Nogent-sur-Seine, France
| | - Tristan Rossignol
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78352 Jouy-en-Josas, France
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Liu HH, Ji XJ, Huang H. Biotechnological applications of Yarrowia lipolytica: Past, present and future. Biotechnol Adv 2015; 33:1522-46. [DOI: 10.1016/j.biotechadv.2015.07.010] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 07/13/2015] [Accepted: 07/29/2015] [Indexed: 01/01/2023]
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Liu S, Wan D, Wang M, Madzak C, Du G, Chen J. Overproduction of pro-transglutaminase from Streptomyces hygroscopicus in Yarrowia lipolytica and its biochemical characterization. BMC Biotechnol 2015; 15:75. [PMID: 26272462 PMCID: PMC4535380 DOI: 10.1186/s12896-015-0193-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background Transglutaminases (TGase), synthesized as a zymogen (pro-TGase) in Streptomyces sp., are important enzymes in food industry. Due to the important applications of TGase in food industry, obtaining robust and food-safe TGase-producing strains has attracted much attention during the past decade. In this study, Streptomyces hygroscopicus pro-TGase was efficiently expressed and secreted by a food-grade host, Yarrowia lipolytica, without antibiotic markers. Results The pro-TGase gene was cloned into integrative vectors pINA1296 (monocopy) and pINA1297 (multicopy), and was used to transform the Y. lipolytica Po1g or Po1h strain, respectively. Expression was driven by a recombinant hp4d promoter and secretion obtained using a XPR2 pre-sequence as a signal peptide. The highest yield of extracellular pro-TGase produced by the recombinant Po1h strain corresponded to 5.3 U/mL of TGase, a level 8.8 fold higher than that obtained using the recombinant Po1g strain. Asparagines in two potential Asn-linked glycosylation sites (Asn160 and Asn355) from pro-TGase were mutated to glutamine individually or simultaneously, yielding the deglycosylated variants N160Q, N355Q, and N160Q/N355Q. The activities of N160Q, N355Q and N160Q/N355Q constructs were respectively 5.3 U/mL, 7.8 U/mL, and 3.0 U/mL, equivalent to 100 %, 147 %, and 57 % of that from wild-type pro-TGase. The TGase yield of N355Q variant was raised to 35.3 U/mL of by using a glycerol feeding strategy in a 3 L fermenter. The optimal pH and temperature of the activated pro-TGase, and of its deglycosylated variants, were in the range of 5.0-6.0 pH and 40-45 °C, respectively. The half-life of the recombinant wild-type pro-TGase at 37 °C reached 34.0 min, and those of the variants were from 24.2 min to 11.5 min. In contrast to the wild-type pro-TGase, all of the variants had decreased specific activities, and both the Km and kcat values of the variants decreased accordingly. Conclusions This study constitutes the first report of the heterologous expression of a pro-TGase in Y. lipolytica, and provides new possibilities for the efficient production of TGases used in food processing.
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Affiliation(s)
- Song Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Lihu Avenue, Wuxi, China.
| | - Dan Wan
- School of Food Science and Technology, Jiangnan University, Lihu Avenue, Wuxi, China.
| | - Miao Wang
- School of Food Science and Technology, Jiangnan University, Lihu Avenue, Wuxi, China.
| | - Catherine Madzak
- INRA, UMR1319 Micalis, Domaine de Vilvert, F-78352, Jouy-en-Josas, France. .,Present address: INRA, UMR 782 Génie et Microbiologie des Procédés Alimentaires, AgroParisTech campus, CBAI, F-78850, Thiverval-Grignon, France.
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Lihu Avenue, Wuxi, China. .,Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Lihu Avenue, Wuxi, China.
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Lihu Avenue, Wuxi, China. .,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Lihu Avenue, Wuxi, China.
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Casas-Godoy L, Meunchan M, Cot M, Duquesne S, Bordes F, Marty A. Yarrowia lipolytica lipase Lip2: An efficient enzyme for the production of concentrates of docosahexaenoic acid ethyl ester. J Biotechnol 2014; 180:30-6. [DOI: 10.1016/j.jbiotec.2014.03.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 03/05/2014] [Accepted: 03/10/2014] [Indexed: 11/15/2022]
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Duquesne S, Bozonnet S, Bordes F, Dumon C, Nicaud JM, Marty A. Construction of a highly active xylanase displaying oleaginous yeast: comparison of anchoring systems. PLoS One 2014; 9:e95128. [PMID: 24743311 PMCID: PMC3990623 DOI: 10.1371/journal.pone.0095128] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 03/24/2014] [Indexed: 11/24/2022] Open
Abstract
Three Yarrowia lipolytica cell wall proteins (YlPir, YlCWP1 and YlCBM) were evaluated for their ability to display the xylanase TxXYN from Thermobacillus xylanilyticus on the cell surface of Y. lipolytica. The fusion proteins were produced in Y. lipolytica JMY1212, a strain engineered for mono-copy chromosomal insertion, and enabling accurate comparison of anchoring systems. The construction using YlPir enabled cell bound xylanase activity to be maximised (71.6 U/g). Although 48% of the activity was released in the supernatant, probably due to proteolysis at the fusion zone, this system is three times more efficient for the anchoring of TxXYN than the YlCWP1 system formerly developed for Y. lipolytica. As far as we know it represents the best displayed xylanase activity ever published. It could be an attractive alternative anchoring system to display enzymes in Y. lipolytica.
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Affiliation(s)
- Sophie Duquesne
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
- * E-mail:
| | - Sophie Bozonnet
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Florence Bordes
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Claire Dumon
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
| | - Jean-Marc Nicaud
- INRA, UMR1319 Micalis, Domaine de Vilvert, Jouy-en-Josas, France
- AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Alain Marty
- Université de Toulouse; INSA, UPS, INP; LISBP, Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France
- CNRS, UMR5504, Toulouse, France
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Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A. Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production. Biotechnol Bioeng 2013; 111:639-53. [PMID: 24284881 DOI: 10.1002/bit.25162] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Hyun Tae Hwang
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Feng Qi
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Chongli Yuan
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Xuebing Zhao
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Doraiswami Ramkrishna
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Dehua Liu
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Arvind Varma
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
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Abstract
The yeast Yarrowia lipolytica presents specific physiological, metabolic and genomic characteristics, which differentiate it from the model yeast Saccharomyces cerevisiae. These properties have led several research groups to use this yeast as a model for basic knowledge. Thanks to the development of advanced genetic tools and -omic approaches, significant progress has been achieved in the understanding of specific biological processes. This review, after a short presentation of this model yeast, will briefly highlight the different use of Y. lipolytica for basic knowledge and the advantages gained by exploiting this non-conventional yeast. Future perspectives in employing this yeast for basic knowledge in the field of RNA splicing and genome evolution, and for the study of lipid metabolism, are also discussed.
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Duquesne S, Bordes F, Fudalej F, Nicaud JM, Marty A. The yeast Yarrowia lipolytica as a generic tool for molecular evolution of enzymes. Methods Mol Biol 2012; 861:301-12. [PMID: 22426726 DOI: 10.1007/978-1-61779-600-5_18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It has been 20 years since strains of the yeast Yarrowia lipolytica were developed for the expression of recombinant proteins as alternative host to the commonly used yeasts, Pichia pastoris and Saccharomyces cerevisiae. Recently, a new strain, JMY1212, was engineered for protein evolution. With this new strain, a very high reproducibility in protein expression level was demonstrated, thus enabling its use for both rational and directed evolution strategies. Indeed, the coefficient of variation was shown to be of 10.7% for the whole process when all the steps are optimized, i.e. transformation of this strain with the gene of interest, cell growth, and protein production under oleic acid induction, and until activity screening assay. The object of this article is to summarize the fruit of these works and show the interest of Y. lipolytica strain JMY1212 for molecular evolution of enzymes, for both rational and directed evolution strategy. Lipase Lip2 from Y. lipolytica is taken here as an example to describe both strategies of molecular evolution. In these two methods, a first step of PCR creates either one targeted (rational design) or various random mutations (directed evolution), and is followed by the incorporation of the expression cassette in the genome of Y. lipolytica. An easy and direct comparison of variant properties is then allowed thanks to the extracellular and reproducible production of variants.
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Affiliation(s)
- Sophie Duquesne
- Equipe de Catalyse et Ingénierie Moléculaire Enzymatique, Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France.
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Piamtongkam R, Duquesne S, Bordes F, Barbe S, André I, Marty A, Chulalaksananukul W. Enantioselectivity of Candida rugosa lipases (Lip1, Lip3, and Lip4) towards 2-bromo phenylacetic acid octyl esters controlled by a single amino acid. Biotechnol Bioeng 2011; 108:1749-56. [DOI: 10.1002/bit.23124] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 02/25/2011] [Accepted: 02/28/2011] [Indexed: 11/11/2022]
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Cambon E, Piamtongkam R, Bordes F, Duquesne S, André I, Marty A. Rationally engineered double substituted variants of Yarrowia lipolytica lipase with enhanced activity coupled with highly inverted enantioselectivity towards 2-bromo phenyl acetic acid esters. Biotechnol Bioeng 2010; 106:852-9. [DOI: 10.1002/bit.22770] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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