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Bokelmann C, Ehsani A, Schaub J, Stiefel F. Deciphering Metabolic Pathways in High-Seeding-Density Fed-Batch Processes for Monoclonal Antibody Production: A Computational Modeling Perspective. Bioengineering (Basel) 2024; 11:331. [PMID: 38671753 PMCID: PMC11048072 DOI: 10.3390/bioengineering11040331] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Due to their high specificity, monoclonal antibodies (mAbs) have garnered significant attention in recent decades, with advancements in production processes, such as high-seeding-density (HSD) strategies, contributing to improved titers. This study provides a thorough investigation of high seeding processes for mAb production in Chinese hamster ovary (CHO) cells, focused on identifying significant metabolites and their interactions. We observed high glycolytic fluxes, the depletion of asparagine, and a shift from lactate production to consumption. Using a metabolic network and flux analysis, we compared the standard fed-batch (STD FB) with HSD cultivations, exploring supplementary lactate and cysteine, and a bolus medium enriched with amino acids. We reconstructed a metabolic network and kinetic models based on the observations and explored the effects of different feeding strategies on CHO cell metabolism. Our findings revealed that the addition of a bolus medium (BM) containing asparagine improved final titers. However, increasing the asparagine concentration in the feed further prevented the lactate shift, indicating a need to find a balance between increased asparagine to counteract limitations and lower asparagine to preserve the shift in lactate metabolism.
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Affiliation(s)
- Carolin Bokelmann
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alireza Ehsani
- Boehringer Ingelheim Pharma GmbH & Co.KG, Launch & Innovation, 88400 Biberach an der Riß, Germany
| | - Jochen Schaub
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, 88400 Biberach an der Riß, Germany
| | - Fabian Stiefel
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Sciences Germany, 88400 Biberach an der Riß, Germany
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2
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Győrgy R, Kostoglou M, Mantalaris A, Georgiadis MC. Development of a multi-scale model to simulate Mesenchymal Stem Cell osteogenic differentiation within hydrogels in a rotating wall bioreactor. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Rodrigues D, Abdalmoaty MR, Jacobsen EW, Chotteau V, Hjalmarsson H. An integrated approach for modeling and identification of perfusion bioreactors via basis flux modes. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Lee D, Jayaraman A, Kwon JS. Identification of cell‐to‐cell heterogeneity through systems engineering approaches. AIChE J 2020. [DOI: 10.1002/aic.16925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dongheon Lee
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
| | - Joseph S.‐I. Kwon
- Artie McFerrin Department of Chemical EngineeringTexas A&M University Texas
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5
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Lee D, Jayaraman A, Sang-Il Kwon J. Identification of a time-varying intracellular signalling model through data clustering and parameter selection: application to NF-[inline-formula removed]B signalling pathway induced by LPS in the presence of BFA. IET Syst Biol 2019; 13:169-179. [PMID: 31318334 PMCID: PMC8687386 DOI: 10.1049/iet-syb.2018.5079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 02/07/2019] [Accepted: 02/14/2019] [Indexed: 01/02/2023] Open
Abstract
Developing a model for a signalling pathway requires several iterations of experimentation and model refinement to obtain an accurate model. However, the implementation of such an approach to model a signalling pathway induced by a poorly-known stimulus can become labour intensive because only limited information on the pathway is available beforehand to formulate an initial model. Therefore, a large number of iterations are required since the initial model is likely to be erroneous. In this work, a numerical scheme is proposed to construct a time-varying model for a signalling pathway induced by a poorly-known stimulus when its nominal model is available in the literature. Here, the nominal model refers to one that describes the signalling dynamics under a well-characterised stimulus. First, global sensitivity analysis is implemented on the nominal model to identify the most important parameters, which are assumed to be piecewise constants. Second, measurement data are clustered to determine temporal subdomains where the parameters take different values. Finally, a least-squares problem is solved to estimate the parameter values in each temporal subdomain. The effectiveness of this approach is illustrated by developing a time-varying model for NF-[inline-formula removed]B signalling dynamics induced by lipopolysaccharide in the presence of brefeldin A.
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Affiliation(s)
- Dongheon Lee
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA
| | - Arul Jayaraman
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Joseph Sang-Il Kwon
- Texas A&M Energy Institute, Texas A&M University, College Station, TX 77843, USA.
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Abstract
Global Sensitivity Analysis (GSA) is a technique that numerically evaluates the significance of model parameters with the aim of reducing the number of parameters that need to be estimated accurately from experimental data. In the work presented herein, we explore different methods and criteria in the sensitivity analysis of a recently developed mathematical model to describe Chinese hamster ovary (CHO) cell metabolism in order to establish a strategic, transferable framework for parameterizing mechanistic cell culture models. For that reason, several types of GSA employing different sampling methods (Sobol’, Pseudo-random and Scrambled-Sobol’), parameter deviations (10%, 30% and 50%) and sensitivity index significance thresholds (0.05, 0.1 and 0.2) were examined. The results were evaluated according to the goodness of fit between the simulation results and experimental data from fed-batch CHO cell cultures. Then, the predictive capability of the model was tested against four different feeding experiments. Parameter value deviation levels proved not to have a significant effect on the results of the sensitivity analysis, while the Sobol’ and Scrambled-Sobol’ sampling methods and a 0.1 significance threshold were found to be the optimum settings. The resulting framework was finally used to calibrate the model for another CHO cell line, resulting in a good overall fit. The results of this work set the basis for the use of a single mechanistic metabolic model that can be easily adapted through the proposed sensitivity analysis method to the behavior of different cell lines and therefore minimize the experimental cost of model development.
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Luna MF, Martínez EC. Optimal design of dynamic experiments in the development of cybernetic models for bioreactors. Chem Eng Res Des 2018. [DOI: 10.1016/j.cherd.2018.05.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Ulonska S, Kroll P, Fricke J, Clemens C, Voges R, Müller MM, Herwig C. Workflow for Target-Oriented Parametrization of an Enhanced Mechanistic Cell Culture Model. Biotechnol J 2017; 13:e1700395. [DOI: 10.1002/biot.201700395] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/19/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Sophia Ulonska
- Institute of Chemical, Environmental and Biological Engineering; TU Wien 1060 Wien Austria
| | - Paul Kroll
- Institute of Chemical, Environmental and Biological Engineering; TU Wien 1060 Wien Austria
- CD Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses; TU Wien 1060 Wien Austria
| | - Jens Fricke
- Institute of Chemical, Environmental and Biological Engineering; TU Wien 1060 Wien Austria
- CD Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses; TU Wien 1060 Wien Austria
| | | | - Raphael Voges
- Boehringer Ingelheim Pharma GmbH & Co. KG; 88400 Biberach Germany
| | - Markus M. Müller
- Boehringer Ingelheim Pharma GmbH & Co. KG; 88400 Biberach Germany
| | - Christoph Herwig
- Institute of Chemical, Environmental and Biological Engineering; TU Wien 1060 Wien Austria
- CD Laboratory on Mechanistic and Physiological Methods for Improved Bioprocesses; TU Wien 1060 Wien Austria
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Younes A, Delay F, Fajraoui N, Fahs M, Mara TA. Global sensitivity analysis and Bayesian parameter inference for solute transport in porous media colonized by biofilms. JOURNAL OF CONTAMINANT HYDROLOGY 2016; 191:1-18. [PMID: 27182791 DOI: 10.1016/j.jconhyd.2016.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 03/22/2016] [Accepted: 04/30/2016] [Indexed: 06/05/2023]
Abstract
The concept of dual flowing continuum is a promising approach for modeling solute transport in porous media that includes biofilm phases. The highly dispersed transit time distributions often generated by these media are taken into consideration by simply stipulating that advection-dispersion transport occurs through both the porous and the biofilm phases. Both phases are coupled but assigned with contrasting hydrodynamic properties. However, the dual flowing continuum suffers from intrinsic equifinality in the sense that the outlet solute concentration can be the result of several parameter sets of the two flowing phases. To assess the applicability of the dual flowing continuum, we investigate how the model behaves with respect to its parameters. For the purpose of this study, a Global Sensitivity Analysis (GSA) and a Statistical Calibration (SC) of model parameters are performed for two transport scenarios that differ by the strength of interaction between the flowing phases. The GSA is shown to be a valuable tool to understand how the complex system behaves. The results indicate that the rate of mass transfer between the two phases is a key parameter of the model behavior and influences the identifiability of the other parameters. For weak mass exchanges, the output concentration is mainly controlled by the velocity in the porous medium and by the porosity of both flowing phases. In the case of large mass exchanges, the kinetics of this exchange also controls the output concentration. The SC results show that transport with large mass exchange between the flowing phases is more likely affected by equifinality than transport with weak exchange. The SC also indicates that weakly sensitive parameters, such as the dispersion in each phase, can be accurately identified. Removing them from calibration procedures is not recommended because it might result in biased estimations of the highly sensitive parameters.
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Affiliation(s)
- A Younes
- LHyGES, Université de Strasbourg/EOST, CNRS, 1 rue Blessig, 67084 Strasbourg, France; IRD UMR LISAH, F-92761 Montpellier, France.
| | - F Delay
- LHyGES, Université de Strasbourg/EOST, CNRS, 1 rue Blessig, 67084 Strasbourg, France
| | - N Fajraoui
- LHyGES, Université de Strasbourg/EOST, CNRS, 1 rue Blessig, 67084 Strasbourg, France
| | - M Fahs
- LHyGES, Université de Strasbourg/EOST, CNRS, 1 rue Blessig, 67084 Strasbourg, France
| | - T A Mara
- Université de La Réunion, PIMENT, 15 Avenue René Cassin, BP 7151, 97715 Moufia, La Réunion, France
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11
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PAROC—An integrated framework and software platform for the optimisation and advanced model-based control of process systems. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2015.02.030] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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García Münzer DG, Kostoglou M, Georgiadis MC, Pistikopoulos EN, Mantalaris A. Cyclin and DNA distributed cell cycle model for GS-NS0 cells. PLoS Comput Biol 2015; 11:e1004062. [PMID: 25723523 PMCID: PMC4344234 DOI: 10.1371/journal.pcbi.1004062] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/26/2014] [Indexed: 01/10/2023] Open
Abstract
Mammalian cell cultures are intrinsically heterogeneous at different scales (molecular to bioreactor). The cell cycle is at the centre of capturing heterogeneity since it plays a critical role in the growth, death, and productivity of mammalian cell cultures. Current cell cycle models use biological variables (mass/volume/age) that are non-mechanistic, and difficult to experimentally determine, to describe cell cycle transition and capture culture heterogeneity. To address this problem, cyclins-key molecules that regulate cell cycle transition-have been utilized. Herein, a novel integrated experimental-modelling platform is presented whereby experimental quantification of key cell cycle metrics (cell cycle timings, cell cycle fractions, and cyclin expression determined by flow cytometry) is used to develop a cyclin and DNA distributed model for the industrially relevant cell line, GS-NS0. Cyclins/DNA synthesis rates were linked to stimulatory/inhibitory factors in the culture medium, which ultimately affect cell growth. Cell antibody productivity was characterized using cell cycle-specific production rates. The solution method delivered fast computational time that renders the model's use suitable for model-based applications. Model structure was studied by global sensitivity analysis (GSA), which identified parameters with a significant effect on the model output, followed by re-estimation of its significant parameters from a control set of batch experiments. A good model fit to the experimental data, both at the cell cycle and viable cell density levels, was observed. The cell population heterogeneity of disturbed (after cell arrest) and undisturbed cell growth was captured proving the versatility of the modelling approach. Cell cycle models able to capture population heterogeneity facilitate in depth understanding of these complex systems and enable systematic formulation of culture strategies to improve growth and productivity. It is envisaged that this modelling approach will pave the model-based development of industrial cell lines and clinical studies.
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Affiliation(s)
- David G. García Münzer
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Margaritis Kostoglou
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Michael C. Georgiadis
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efstratios N. Pistikopoulos
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Athanasios Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
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13
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Niu H, Leak D, Shah N, Kontoravdi C. Metabolic characterization and modeling of fermentation process of an engineered Geobacillus thermoglucosidasius strain for bioethanol production with gas stripping. Chem Eng Sci 2015. [DOI: 10.1016/j.ces.2014.09.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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García Münzer D, Ivarsson M, Usaku C, Habicher T, Soos M, Morbidelli M, Pistikopoulos E, Mantalaris A. An unstructured model of metabolic and temperature dependent cell cycle arrest in hybridoma batch and fed-batch cultures. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Kontoravdi C. Systematic methodology for the development of mathematical models for biological processes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2014; 1073:177-90. [PMID: 23996448 DOI: 10.1007/978-1-62703-625-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Synthetic biology gives researchers the opportunity to rationally (re-)design cellular activities to achieve a desired function. The design of networks of pathways towards accomplishing this calls for the application of engineering principles, often using model-based tools. Success heavily depends on model reliability. Herein, we present a systematic methodology for developing predictive models comprising model formulation considerations, global sensitivity analysis, model reduction (for highly complex models or where experimental data are limited), optimal experimental design for parameter estimation, and predictive capability checking. Its efficacy and validity are demonstrated using an example from bioprocessing. This approach systematizes the process of developing reliable mathematical models at a minimum experimental cost, enabling in silico simulation and optimization.
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Affiliation(s)
- Cleo Kontoravdi
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, UK
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16
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Jedrzejewski PM, del Val IJ, Constantinou A, Dell A, Haslam SM, Polizzi KM, Kontoravdi C. Towards controlling the glycoform: a model framework linking extracellular metabolites to antibody glycosylation. Int J Mol Sci 2014; 15:4492-522. [PMID: 24637934 PMCID: PMC3975410 DOI: 10.3390/ijms15034492] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 02/07/2014] [Accepted: 02/21/2014] [Indexed: 01/23/2023] Open
Abstract
Glycoproteins represent the largest group of the growing number of biologically-derived medicines. The associated glycan structures and their distribution are known to have a large impact on pharmacokinetics. A modelling framework was developed to provide a link from the extracellular environment and its effect on intracellular metabolites to the distribution of glycans on the constant region of an antibody product. The main focus of this work is the mechanistic in silico reconstruction of the nucleotide sugar donor (NSD) metabolic network by means of 34 species mass balances and the saturation kinetics rates of the 60 metabolic reactions involved. NSDs are the co-substrates of the glycosylation process in the Golgi apparatus and their simulated dynamic intracellular concentration profiles were linked to an existing model describing the distribution of N-linked glycan structures of the antibody constant region. The modelling framework also describes the growth dynamics of the cell population by means of modified Monod kinetics. Simulation results match well to experimental data from a murine hybridoma cell line. The result is a modelling platform which is able to describe the product glycoform based on extracellular conditions. It represents a first step towards the in silico prediction of the glycoform of a biotherapeutic and provides a platform for the optimisation of bioprocess conditions with respect to product quality.
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Affiliation(s)
- Philip M Jedrzejewski
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.
| | - Ioscani Jimenez del Val
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.
| | | | - Anne Dell
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Karen M Polizzi
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
| | - Cleo Kontoravdi
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, UK.
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Baumuratova T, Dobre S, Bastogne T, Sauter T. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition. PLoS One 2013; 8:e82973. [PMID: 24367574 PMCID: PMC3867467 DOI: 10.1371/journal.pone.0082973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA - a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits.
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Affiliation(s)
- Tatiana Baumuratova
- Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg, Luxembourg
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
- * E-mail:
| | - Simona Dobre
- ISL, French-German Research Institute of Saint-Louis, Saint-Louis, France
| | - Thierry Bastogne
- Université de Lorraine, CRAN, UMR 7039, Vandœuvre-lès-Nancy, France
- CNRS, CRAN, UMR 7039, Vandœuvre-lès-Nancy, France
- INRIA, BIGS, Vandœuvre-lès-Nancy, France
| | - Thomas Sauter
- Systems Biology Group, Life Sciences Research Unit, University of Luxembourg, Luxembourg, Luxembourg
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Metabolic pathway analysis and reduction for mammalian cell cultures—Towards macroscopic modeling. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.07.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Anesiadis N, Kobayashi H, Cluett WR, Mahadevan R. Analysis and design of a genetic circuit for dynamic metabolic engineering. ACS Synth Biol 2013; 2:442-52. [PMID: 23654263 DOI: 10.1021/sb300129j] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent advances in synthetic biology have equipped us with new tools for bioprocess optimization at the genetic level. Previously, we have presented an integrated in silico design for the dynamic control of gene expression based on a density-sensing unit and a genetic toggle switch. In the present paper, analysis of a serine-producing Escherichia coli mutant shows that an instantaneous ON-OFF switch leads to a maximum theoretical productivity improvement of 29.6% compared to the mutant. To further the design, global sensitivity analysis is applied here to a mathematical model of serine production in E. coli coupled with a genetic circuit. The model of the quorum sensing and the toggle switch involves 13 parameters of which 3 are identified as having a significant effect on serine concentration. Simulations conducted in this reduced parameter space further identified the optimal ranges for these 3 key parameters to achieve productivity values close to the maximum theoretical values. This analysis can now be used to guide the experimental implementation of a dynamic metabolic engineering strategy and reduce the time required to design the genetic circuit components.
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Affiliation(s)
- Nikolaos Anesiadis
- Department
of Chemical Engineering
and Applied Chemistry, University of Toronto, Canada, M5S 3E5
| | | | - William R. Cluett
- Department
of Chemical Engineering
and Applied Chemistry, University of Toronto, Canada, M5S 3E5
| | - Radhakrishnan Mahadevan
- Department
of Chemical Engineering
and Applied Chemistry, University of Toronto, Canada, M5S 3E5
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, Canada, M5S 3G9
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Chakrabarty A, Buzzard GT, Rundell AE. Model-based design of experiments for cellular processes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:181-203. [PMID: 23293047 DOI: 10.1002/wsbm.1204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ankush Chakrabarty
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
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21
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Chu Y, Hahn J. Necessary condition for applying experimental design criteria to global sensitivity analysis results. Comput Chem Eng 2013. [DOI: 10.1016/j.compchemeng.2012.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Mead EJ, Chiverton LM, Spurgeon SK, Martin EB, Montague GA, Smales CM, von der Haar T. Experimental and in silico modelling analyses of the gene expression pathway for recombinant antibody and by-product production in NS0 cell lines. PLoS One 2012; 7:e47422. [PMID: 23071804 PMCID: PMC3468484 DOI: 10.1371/journal.pone.0047422] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 09/17/2012] [Indexed: 11/18/2022] Open
Abstract
Monoclonal antibodies are commercially important, high value biotherapeutic drugs used in the treatment of a variety of diseases. These complex molecules consist of two heavy chain and two light chain polypeptides covalently linked by disulphide bonds. They are usually expressed as recombinant proteins from cultured mammalian cells, which are capable of correctly modifying, folding and assembling the polypeptide chains into the native quaternary structure. Such recombinant cell lines often vary in the amounts of product produced and in the heterogeneity of the secreted products. The biological mechanisms of this variation are not fully defined. Here we have utilised experimental and modelling strategies to characterise and define the biology underpinning product heterogeneity in cell lines exhibiting varying antibody expression levels, and then experimentally validated these models. In undertaking these studies we applied and validated biochemical (rate-constant based) and engineering (nonlinear) models of antibody expression to experimental data from four NS0 cell lines with different IgG4 secretion rates. The models predict that export of the full antibody and its fragments are intrinsically linked, and cannot therefore be manipulated individually at the level of the secretory machinery. Instead, the models highlight strategies for the manipulation at the precursor species level to increase recombinant protein yields in both high and low producing cell lines. The models also highlight cell line specific limitations in the antibody expression pathway.
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Affiliation(s)
- Emma J. Mead
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- Centre for Molecular Processing, University of Kent, Canterbury, United Kingdom
- * E-mail: (EJM); (CMS); (TvdH)
| | - Lesley M. Chiverton
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- Centre for Molecular Processing, University of Kent, Canterbury, United Kingdom
| | - Sarah K. Spurgeon
- School of Engineering and Digital Arts, University of Kent, Canterbury, United Kingdom
- Centre for Molecular Processing, University of Kent, Canterbury, United Kingdom
| | - Elaine B. Martin
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle, United Kingdom
| | - Gary A. Montague
- School of Chemical Engineering and Advanced Materials, Newcastle University, Newcastle, United Kingdom
| | - C. Mark Smales
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- Centre for Molecular Processing, University of Kent, Canterbury, United Kingdom
- * E-mail: (EJM); (CMS); (TvdH)
| | - Tobias von der Haar
- School of Biosciences, University of Kent, Canterbury, United Kingdom
- Centre for Molecular Processing, University of Kent, Canterbury, United Kingdom
- * E-mail: (EJM); (CMS); (TvdH)
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Ho Y, Kiparissides A, Pistikopoulos EN, Mantalaris A. Computational approach for understanding and improving GS-NS0 antibody production under hyperosmotic conditions. J Biosci Bioeng 2012; 113:88-98. [DOI: 10.1016/j.jbiosc.2011.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/21/2011] [Accepted: 08/22/2011] [Indexed: 02/02/2023]
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Dahodwala H, Nowey M, Mitina T, Sharfstein ST. Effects of clonal variation on growth, metabolism, and productivity in response to trophic factor stimulation: a study of Chinese hamster ovary cells producing a recombinant monoclonal antibody. Cytotechnology 2012; 64:27-41. [PMID: 21822681 PMCID: PMC3261449 DOI: 10.1007/s10616-011-9388-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 07/27/2011] [Indexed: 10/17/2022] Open
Abstract
The growth, metabolism, and productivity of five Chinese hamster ovary (CHO) clones were explored in response to stimulation with insulin (5 mg/L) and LONG(®)R(3)IGF-I (20 μg/L or 100 μg/L). All five clones were derived from the same parental CHO cell line (DG44) and produced the same recombinant monoclonal antibody, with varying specific productivities. There was no uniform response among the clones to stimulation with the different trophic factors. One of the high productivity clones (clone D) exhibited significantly better growth in response to LONG(®)R(3)IGF-I; whereas the other clones showed equivalent or slightly better growth in the presence of insulin. Three out of the five clones had higher specific productivities in the presence of insulin (although not statistically significant); one was invariant, and the final clone exhibited slightly higher specific productivity in the presence of LONG(®)R(3)IGF-I. Total product titers exhibited moderate variation between culture conditions, again with neither trophic factor being clearly superior. Overall product titers were affected by variations in both integrated viable cell density and specific productivity. Nutrient uptake and metabolite generation patterns varied strongly between clones and much less with culture conditions. These results point to the need for careful clonal analysis when selecting clones, particularly for platform processes where media and culture conditions are predetermined.
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Affiliation(s)
- Hussain Dahodwala
- Biochemistry and Biophysics Program, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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Abstract
In this feature, leading researchers in the field of microbial biotechnology speculate on the technical and conceptual developments that will drive innovative research and open new vistas over the next few years.
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Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. MOLECULAR BIOSYSTEMS 2010; 6:1890-900. [PMID: 20556289 PMCID: PMC3505121 DOI: 10.1039/b918098b] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational models are increasingly used to understand and predict complex biological phenomena. These models contain many unknown parameters, at least some of which are difficult to measure directly, and instead are estimated by fitting to time-course data. Previous work has suggested that even with precise data sets, many parameters are unknowable by trajectory measurements. We examined this question in the context of a pathway model of epidermal growth factor (EGF) and neuronal growth factor (NGF) signaling. Computationally, we examined a palette of experimental perturbations that included different doses of EGF and NGF as well as single and multiple gene knockdowns and overexpressions. While no single experiment could accurately estimate all of the parameters, experimental design methodology identified a set of five complementary experiments that could. These results suggest optimism for the prospects for calibrating even large models, that the success of parameter estimation is intimately linked to the experimental perturbations used, and that experimental design methodology is important for parameter fitting of biological models and likely for the accuracy that can be expected from them.
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Affiliation(s)
- Joshua F. Apgar
- Department of Biological Engineering
- Computer Science and Artificial Intelligence Laboratory
| | - David K. Witmer
- Computer Science and Artificial Intelligence Laboratory
- Department of Electrical Engineering and Computer Science
| | - Forest M. White
- Department of Biological Engineering
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bruce Tidor
- Department of Biological Engineering
- Computer Science and Artificial Intelligence Laboratory
- Department of Electrical Engineering and Computer Science
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O'Callaghan PM, McLeod J, Pybus LP, Lovelady CS, Wilkinson SJ, Racher AJ, Porter A, James DC. Cell line-specific control of recombinant monoclonal antibody production by CHO cells. Biotechnol Bioeng 2010; 106:938-51. [DOI: 10.1002/bit.22769] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Chu Y, Hahn J. Quantitative Optimal Experimental Design Using Global Sensitivity Analysis via Quasi-Linearization. Ind Eng Chem Res 2010. [DOI: 10.1021/ie9009827] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yunfei Chu
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
| | - Juergen Hahn
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122
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Koutinas M, Kiparissides A, Lam MC, Silva-Rocha R, de Lorenzo V, Martins dos Santos VA, Pistikopoulos EN, Mantalaris A. Combining Genetic Circuit and Microbial Growth Kinetic Models: A Challenge for Biological Modelling. COMPUTER AIDED CHEMICAL ENGINEERING 2010. [DOI: 10.1016/s1570-7946(10)28051-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Koutinas M, Lam MC, Kiparissides A, Silva-Rocha R, Godinho M, Livingston AG, Pistikopoulos EN, De Lorenzo V, Dos Santos VAPM, Mantalaris A. The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol 2009; 12:1705-18. [DOI: 10.1111/j.1462-2920.2010.02245.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Kiparissides A, Kucherenko SS, Mantalaris A, Pistikopoulos EN. Global Sensitivity Analysis Challenges in Biological Systems Modeling. Ind Eng Chem Res 2009. [DOI: 10.1021/ie900139x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Kiparissides
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - S. S. Kucherenko
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - A. Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - E. N. Pistikopoulos
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
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Liu P, Pistikopoulos EN, Li Z. A mixed-integer optimization approach for polygeneration energy systems design. Comput Chem Eng 2009. [DOI: 10.1016/j.compchemeng.2008.08.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yue H, Brown M, He F, Jia J, Kell DB. Sensitivity analysis and robust experimental design of a signal transduction pathway system. INT J CHEM KINET 2008. [DOI: 10.1002/kin.20369] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Franceschini G, Macchietto S. Model-based design of experiments for parameter precision: State of the art. Chem Eng Sci 2008. [DOI: 10.1016/j.ces.2007.11.034] [Citation(s) in RCA: 297] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Application of global sensitivity analysis to biological models. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s1570-7946(08)80120-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
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Acosta ML, Sánchez A, García F, Contreras A, Molina E. Analysis of kinetic, stoichiometry and regulation of glucose and glutamine metabolism in hybridoma batch cultures using logistic equations. Cytotechnology 2007; 54:189-200. [PMID: 19003011 DOI: 10.1007/s10616-007-9089-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 07/25/2007] [Indexed: 10/22/2022] Open
Abstract
Batch cultures were carried out to study the kinetic, stoichiometry, and regulation of glucose and glutamine metabolism of a murine hybridoma line. Asymmetric logistic equations (ALEs) were used to fit total and viable cell density, and nutrient and metabolite/product concentrations. Since these equations were analytically differentiable, specific rates and yield coefficients were readily calculated. Asymmetric logistic equations described satisfactorily uncontrolled batch cultures, including death phase. Specific growth rate showed a Monod-type dependence on initial glucose and glutamine concentrations. Yield coefficients of cell and lactate from glucose, and cell and ammonium from glutamine were all found to change dramatically at low residual glucose and glutamine concentrations. Under stoichiometric glucose limitation, the glucose-to-cell yield increased and glucose-to-lactate yield decreased, indicating a metabolic shift. Under stoichiometric glutamine limitation the glutamine-to-cell and glutamine-to-ammonium yields increased, but also glucose-to-cell yield increased and the glucose-to-lactate yield decreased. Monoclonal antibody production was mainly non-growth associated, independently of glucose and glutamine levels.
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Affiliation(s)
- María Lourdes Acosta
- Department of Chemical Engineering, University of Almería, Almería, 04120, Spain
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Kontoravdi C, Asprey SP, Pistikopoulos EN, Mantalaris A. Development of a dynamic model of monoclonal antibody production and glycosylation for product quality monitoring. Comput Chem Eng 2007. [DOI: 10.1016/j.compchemeng.2006.04.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Rodriguez-Fernandez M, Kucherenko S, Pantelides C, Shah N. Optimal experimental design based on global sensitivity analysis. COMPUTER AIDED CHEMICAL ENGINEERING 2007. [DOI: 10.1016/s1570-7946(07)80034-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Surrogate Model-Based Optimization Framework: A Case Study in Aerospace Design. STUDIES IN COMPUTATIONAL INTELLIGENCE 2007. [DOI: 10.1007/978-3-540-49774-5_14] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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