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Fink M, Schimek C, Cserjan-Puschmann M, Reinisch D, Brocard C, Hahn R, Striedner G. Integrated process development: The key to improve Fab production in E. coli. Biotechnol J 2021; 16:e2000562. [PMID: 33580620 DOI: 10.1002/biot.202000562] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/04/2021] [Accepted: 02/04/2021] [Indexed: 11/09/2022]
Abstract
Bioprocess development and optimization is a challenging, costly, and time-consuming effort. In this multidisciplinary task, upstream processing (USP) and downstream processing (DSP) are conventionally considered distinct disciplines. This consideration fosters "one-way" optimization disregarding interdependencies between unit operations; thus, the full potential of the process chain cannot be achieved. Therefore, it is necessary to fully integrate USP and DSP process development to provide balanced biotechnological production processes. The aim of the present study was to investigate how different host/secretory signal/antigen binding fragment (Fab) combinations in E. coli expression systems influence USP, primary recovery performance and the final product quality. We ran identical fed-batch cultivations with 16 different expression clones to study growth and product formation kinetics, as well as centrifugation efficiency, viscosity, extracellular DNA, and endotoxin content, important parameters in DSP. We observed a severe influence on cell growth, product titer, extracellular product, and cell lysis, accompanied by a significant impact on the analyzed parameters of DSP performance. Our results provide the basis for future research on integrated process development considering interdependencies between USP and DSP; however, individual products need to be considered specifically. These interdependencies need to be understood for rational decision-making and efficient process development in research and industry.
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Affiliation(s)
- Mathias Fink
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Schimek
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Monika Cserjan-Puschmann
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | | | | | - Rainer Hahn
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gerald Striedner
- Christian Doppler Laboratory for production of next-level biopharmaceuticals in E. coli, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Malik S, Hagopian J, Mohite S, Lintong C, Stoffels L, Giannakopoulos S, Beckett R, Leung C, Ruiz J, Cruz M, Parker B. Robotic Extrusion of Algae-Laden Hydrogels for Large-Scale Applications. GLOBAL CHALLENGES (HOBOKEN, NJ) 2020; 4:1900064. [PMID: 31956429 PMCID: PMC6957016 DOI: 10.1002/gch2.201900064] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Indexed: 05/14/2023]
Abstract
A bioprinting technique for large-scale, custom-printed immobilization of microalgae is developed for potential applications within architecture and the built environment. Alginate-based hydrogels with various rheology modifying polymers and varying water percentages are characterized to establish a window of operation suitable for layer-by-layer deposition on a large scale. Hydrogels formulated with methylcellulose and carrageenan, with water percentages ranging from 80% to 92.5%, demonstrate a dominant viscoelastic solid-like property with G' > G″ and a low phase angle, making them the most suitable for extrusion-based printing. A custom multimaterial pneumatic extrusion system is developed to be attached on the end effector of an industrial multiaxis robot arm, allowing precision-based numerically controlled layered deposition of the viscous hydrogel. The relationship between the various printing parameters, namely air pressure, material viscosity, viscoelasticity, feed rate, printing distance, nozzle diameter, and the speed of printing, are characterized to achieve the desired resolution of the component. Printed prototypes are postcured in CaCl2 via crosslinking. Biocompatibility tests show that cells can survive for 21 days after printing the constructs. To demonstrate the methodology for scale-up, a 1000 × 500 mm fibrous hydrogel panel is additively deposited with 3 different hydrogels with varying water percentages.
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Affiliation(s)
- Shneel Malik
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Julie Hagopian
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Sanika Mohite
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Cao Lintong
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1H 0AHUK
| | - Laura Stoffels
- Institute of Structural and Molecular BiologyUniversity College LondonLondonWC1E 6BTUK
| | | | - Richard Beckett
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Christopher Leung
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Javier Ruiz
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Marcos Cruz
- Bartlett School of ArchitectureUniversity College LondonLondonWC1E 6BTUK
| | - Brenda Parker
- Department of Biochemical EngineeringBernard Katz BuildingUniversity College LondonLondonWC1H 0AHUK
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Stoffels L, Finlan A, Mannall G, Purton S, Parker B. Downstream Processing of Chlamydomonas reinhardtii TN72 for Recombinant Protein Recovery. Front Bioeng Biotechnol 2019; 7:383. [PMID: 31867315 PMCID: PMC6908742 DOI: 10.3389/fbioe.2019.00383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
The green microalga Chlamydomonas reinhardtii is under development as a production host for recombinant proteins and whole-cell therapeutics. In particular, the cell wall-reduced strain TN72 is used as a model organism for protein expression and algal synthetic biology. However, the bioprocessing characteristics of TN72 and other C. reinhardtii strains have yet to be examined. Here we use a TN72 strain expressing a protein-based antibiotic (Pal) to study the scale-up of cell harvest and product recovery. Cell harvest was examined with 100L cultures in two intermittent-discharge continuous-flow disc-stack centrifuges at flow rates of 150–250 L.h−1, as well as with an ultra scale-down (USD) mimic of the centrifuges. Solids recovery exceeded 99.5% and the loss of product to the supernatant was below 2–3%. TN72 is intact following the high shear conditions of the feed zone, however discharge from both disc-stack centrifuges resulted in full cell breakage and in the case of Pal, partial degradation in the subsequent hours. We demonstrated that shake flask cultivation and the USD centrifuge technique can be used to predict the pilot-scale clarification efficiency and product release at the centrifuge inlet for TN72, but not the cell breakage on discharge. This study outlines a number of challenges for scale-up of recombinant protein production in the microalgal host in particular for whole cell therapeutics, but also opportunities for the bioprocessing of intracellular products from TN72.
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Affiliation(s)
- Laura Stoffels
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, United Kingdom.,Algal Research Group, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Arran Finlan
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, United Kingdom
| | - Gareth Mannall
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, United Kingdom
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Brenda Parker
- Department of Biochemical Engineering, Bernard Katz Building, University College London, London, United Kingdom
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pH conditioning is a crucial step in primary recovery - A case study for a recombinant Fab from E. coli. Protein Expr Purif 2019; 165:105504. [PMID: 31560987 DOI: 10.1016/j.pep.2019.105504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/23/2019] [Indexed: 11/23/2022]
Abstract
Primary recovery of recombinant proteins from E. coli often describes a major challenge in downstream processing. After product release, the target protein usually accounts for only a small amount of total protein and has to be separated from a complex mixture of host cell proteins (HCPs) and non-proteinogenic impurities, such as DNA and lipids. Non-optimized procedures as well as unfavorable conditions at the extraction step and conditioning cause significant product loss already prior capture. In this study, we investigated pH conditioning during primary recovery for a subsequent cation exchange chromatography (CEX)-based capture of a recombinant Fab produced in E. coli. We showed that pH ≤ 5.0, which is necessary for CEX, led to high product loss due to protein precipitation during cell disruption and pH conditioning. Thus, we developed a procedure that resulted in a 25% increased Fab recovery prior capture based on simple re-arrangement of process steps and the use of a low-cost stabilizing agent. Summarizing, we show the huge potential for simple and cheap improvement of overall downstream process recovery by optimization of pH conditioning during primary product recovery.
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Walther C, Kellner M, Berkemeyer M, Brocard C, Dürauer A. Integrated process development—a robust, rapid method for inclusion body harvesting and processing at the microscale level. Prep Biochem Biotechnol 2017; 47:874-880. [DOI: 10.1080/10826068.2017.1350978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Cornelia Walther
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
- Biopharma Process Science Boehringer-Ingelheim Regional Center Vienna, Vienna, Austria
| | - Martin Kellner
- Biopharma Process Science Boehringer-Ingelheim Regional Center Vienna, Vienna, Austria
| | - Matthias Berkemeyer
- Biopharma Process Science Boehringer-Ingelheim Regional Center Vienna, Vienna, Austria
| | - Cécile Brocard
- Biopharma Process Science Boehringer-Ingelheim Regional Center Vienna, Vienna, Austria
| | - Astrid Dürauer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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Walther C, Kellner M, Berkemeyer M, Brocard C, Dürauer A. A microscale bacterial cell disruption technique as first step for automated and miniaturized process development. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Abstract
Escherichia coli, Saccharomyces cerevisiae, and Pichia pastoris are the standard platforms for biopharmaceutical production with 40% of all between 2010 to 2014 approved protein drugs produced in those microbial hosts. Typically, products overexpressed E. coli and S. cerevisiae remain in the cytosol or are secreted into the periplasm. Consequently, efficient cell disruption is essential for high product recovery during microbial production. Process development platforms at microscale are essential to shorten time to market. While high-pressure homogenization is the industry standard for cell disruption at large scale this method is not practicable for experiments in microscale. This review describes microscale methods for cell disruption at scales as low as 200 µL. Strategies for automation, parallelization and miniaturization, as well as comparability of the results at this scale to high pressure homogenization are considered as those criteria decide which methods are most suited for scale down. Those aspects are discussed in detail for protein overexpression in E. coli and yeast but also the relevance for alternative products and host such as microalgae are taken into account. The authors conclude that bead milling is the best comparable microscale method to large scale high-pressure homogenization and therefore the most suitable technique for automated process development of microbial hosts with the exception of pDNA production.
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Affiliation(s)
- Cornelia Walther
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Boehringer-Ingelheim Regional Center Vienna, Vienna, Austria
| | - Astrid Dürauer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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Newton JM, Vlahopoulou J, Zhou Y. Investigating and modelling the effects of cell lysis on the rheological properties of fermentation broths. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Ultra scale-down approaches to enhance the creation of bioprocesses at scale: impacts of process shear stress and early recovery stages. Curr Opin Chem Eng 2016. [DOI: 10.1016/j.coche.2016.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Newton JM, Schofield D, Vlahopoulou J, Zhou Y. Detecting cell lysis using viscosity monitoring in E. coli fermentation to prevent product loss. Biotechnol Prog 2016; 32:1069-76. [PMID: 27111912 PMCID: PMC4999026 DOI: 10.1002/btpr.2292] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/14/2016] [Indexed: 11/10/2022]
Abstract
Monitoring the physical or chemical properties of cell broths to infer cell status is often challenging due to the complex nature of the broth. Key factors indicative of cell status include cell density, cell viability, product leakage, and DNA release to the fermentation broth. The rapid and accurate prediction of cell status for hosts with intracellular protein products can minimise product loss due to leakage at the onset of cell lysis in fermentation. This article reports the rheological examination of an industrially relevant E. coli fermentation producing antibody fragments (Fab'). Viscosity monitoring showed an increase in viscosity during the exponential phase in relation to the cell density increase, a relatively flat profile in the stationary phase, followed by a rapid increase which correlated well with product loss, DNA release and loss of cell viability. This phenomenon was observed over several fermentations that a 25% increase in broth viscosity (using induction-point viscosity as a reference) indicated 10% product loss. Our results suggest that viscosity can accurately detect cell lysis and product leakage in postinduction cell cultures, and can identify cell lysis earlier than several other common fermentation monitoring techniques. This work demonstrates the utility of rapidly monitoring the physical properties of fermentation broths, and that viscosity monitoring has the potential to be a tool for process development to determine the optimal harvest time and minimise product loss. © 2016 The Authors. Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers, 32:1069-1076, 2016.
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Affiliation(s)
- Joseph M Newton
- Dept. of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Desmond Schofield
- Dept. of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, U.K
| | - Joanna Vlahopoulou
- Research & Development, Procellia Ltd, Netpark Incubator, Thomas Wright Way, Sedgefield, County Durham, TS21 3FD, U.K
| | - Yuhong Zhou
- Dept. of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, U.K
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11
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Voulgaris I, Chatel A, Hoare M, Finka G, Uden M. Evaluation of options for harvest of a recombinant E. Coli fermentation producing a domain antibody using ultra scale-down techniques and pilot-scale verification. Biotechnol Prog 2016; 32:382-92. [PMID: 26698375 PMCID: PMC4991298 DOI: 10.1002/btpr.2220] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 11/06/2015] [Indexed: 01/21/2023]
Abstract
Ultra scale‐down (USD) methods operating at the millilitre scale were used to characterise full‐scale processing of E. coli fermentation broths autolysed to different extents for release of a domain antibody. The focus was on the primary clarification stages involving continuous centrifugation followed by depth filtration. The performance of this sequence was predicted by USD studies to decrease significantly with increased extents of cell lysis. The use of polyethyleneimine reagent was studied to treat the lysed cell broth by precipitation of soluble contaminants such as DNA and flocculation of cell debris material. The USD studies were used to predict the impact of this treatment on the performance and here it was found that the fermentation could be run to maximum productivity using an acceptable clarification process (e.g., a centrifugation stage operating at 0.11 L/m2 equivalent gravity settling area per hour followed by a resultant required depth filter area of 0.07 m2/L supernatant). A range of USD predictions was verified at the pilot scale for centrifugation followed by depth filtration. © 2016 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 32:382–392, 2016
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Affiliation(s)
- Ioannis Voulgaris
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, UCL, Gower St, London, WC1E 6BT.,Biopharm Process Research, BioPharm R&D, GlaxoSmithKline, R&D, Stevenage, SG1 2NY
| | - Alex Chatel
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, UCL, Gower St, London, WC1E 6BT
| | - Mike Hoare
- Dept. of Biochemical Engineering, The Advanced Centre for Biochemical Engineering, UCL, Gower St, London, WC1E 6BT
| | - Gary Finka
- Biopharm Process Research, BioPharm R&D, GlaxoSmithKline, R&D, Stevenage, SG1 2NY
| | - Mark Uden
- Biopharm Process Research, BioPharm R&D, GlaxoSmithKline, R&D, Stevenage, SG1 2NY
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Enhancing the selective extracellular location of a recombinant E. coli domain antibody by management of fermentation conditions. Appl Microbiol Biotechnol 2015; 99:8441-53. [PMID: 26184976 PMCID: PMC4768232 DOI: 10.1007/s00253-015-6799-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 06/22/2015] [Accepted: 06/24/2015] [Indexed: 01/26/2023]
Abstract
The preparation of a recombinant protein using Escherichia coli often involves a challenging primary recovery sequence. This is due to the inability to secrete the protein to the extracellular space without a significant degree of cell lysis. This results in the release of nucleic acids, leading to a high viscosity, difficulty to clarify, broth and also to contamination with cell materials such as lipopolysaccharides and host cell proteins. In this paper, we present different fermentation strategies to facilitate the recovery of a V H domain antibody (13.1 kDa) by directing it selectively to the extracellular space and changing the balance between domain antibody to nucleic acid release. The manipulation of the cell growth rate in order to increase the outer cell membrane permeability gave a small ~1.5-fold improvement in released domain antibody to nucleic acid ratio without overall loss of yield. The introduction during fermentation of release agents such as EDTA gave no improvement in the ratio of released domain antibody to nucleic acid and a loss of overall productivity. The use of polyethyleneimine (PEI) during fermentation was with the aim to (a) permeabilise the outer bacterial membrane to release selectively domain antibody and (b) remove selectively by precipitation nucleic acids released during cell lysis. This strategy resulted in up to ~4-fold increase in the ratio of domain antibody to soluble nucleic acid with no reduction in domain antibody overall titre. In addition, a reduction in host cell protein contamination was achieved and there was no increase in endotoxin levels. Similar results were demonstrated with a range of other antibody products prepared in E. coli.
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Formenti LR, Nørregaard A, Bolic A, Hernandez DQ, Hagemann T, Heins AL, Larsson H, Mears L, Mauricio-Iglesias M, Krühne U, Gernaey KV. Challenges in industrial fermentation technology research. Biotechnol J 2014; 9:727-38. [PMID: 24846823 DOI: 10.1002/biot.201300236] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/01/2014] [Accepted: 04/23/2014] [Indexed: 11/06/2022]
Abstract
Industrial fermentation processes are increasingly popular, and are considered an important technological asset for reducing our dependence on chemicals and products produced from fossil fuels. However, despite their increasing popularity, fermentation processes have not yet reached the same maturity as traditional chemical processes, particularly when it comes to using engineering tools such as mathematical models and optimization techniques. This perspective starts with a brief overview of these engineering tools. However, the main focus is on a description of some of the most important engineering challenges: scaling up and scaling down fermentation processes, the influence of morphology on broth rheology and mass transfer, and establishing novel sensors to measure and control insightful process parameters. The greatest emphasis is on the challenges posed by filamentous fungi, because of their wide applications as cell factories and therefore their relevance in a White Biotechnology context. Computational fluid dynamics (CFD) is introduced as a promising tool that can be used to support the scaling up and scaling down of bioreactors, and for studying mixing and the potential occurrence of gradients in a tank.
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Affiliation(s)
- Luca Riccardo Formenti
- Department of Chemical and Biochemical Engineering, Technical University of Denmark (DTU), Lyngby, Denmark
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