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Van Zyl WF, Van Staden AD, Dicks LMT, Trindade M. Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli. Microb Cell Fact 2023; 22:149. [PMID: 37559122 PMCID: PMC10413542 DOI: 10.1186/s12934-023-02162-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/29/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Lanthipeptides are a rapidly expanding family of ribosomally synthesized and post-translationally modified natural compounds with diverse biological functions. Lanthipeptide structural and biosynthetic genes can readily be identified in genomic datasets, which provides a substantial repository for unique peptides with a wide range of potentially novel bioactivities. To realize this potential efficiently optimized heterologous production systems are required. However, only a few class I lanthipeptides have been successfully expressed using Escherichia coli as heterologous producer. This may be attributed to difficulties experienced in the co-expression of structural genes and multiple processing genes as well as complex optimization experiments. RESULTS Here, an optimized modular plasmid system is presented for the complete biosynthesis for each of the class I lanthipeptides nisin and clausin, in E. coli. Genes encoding precursor lanthipeptides were fused to the gene encoding the mCherry red fluorescent protein and co-expressed along with the required synthetases from the respective operons. Antimicrobially active nisin and clausin were proteolytically liberated from the expressed mCherry fusions. The mCherry-NisA expression system combined with in vivo fluorescence monitoring was used to elucidate the effect of culture media composition, promoter arrangement, and culture conditions including choice of growth media and inducer agents on the heterologous expression of the class I lanthipeptides. To evaluate the promiscuity of the clausin biosynthetic enzymes, the optimized clausin expression system was used for the heterologous expression of epidermin. CONCLUSION We succeeded in developing novel mCherry-fusion based plug and play heterologous expression systems to produce two different subgroups of class I lanthipeptides. Fully modified Pre-NisA, Pre-ClausA and Pre-EpiA fused to the mCherry fluorescence gene was purified from the Gram-negative host E. coli BL21 (DE3). Our study demonstrates the potential of using in vivo fluorescence as a platform to evaluate the expression of mCherry-fused lanthipeptides in E. coli. This allowed a substantial reduction in optimization time, since expression could be monitored in real-time, without the need for extensive and laborious purification steps or the use of in vitro activity assays. The optimized heterologous expression systems developed in this study may be employed in future studies for the scalable expression of novel NisA derivatives, or novel genome mined derivatives of ClausA and other class I lanthipeptides in E. coli.
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Affiliation(s)
- Winschau F Van Zyl
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa.
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, South Africa.
| | - Anton D Van Staden
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
- Division of Clinical Pharmacology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Cape Town, South Africa
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, University of the Western Cape, Cape Town, South Africa
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Effect of temperature on the production of a recombinant antivenom in fed-batch mode. Appl Microbiol Biotechnol 2021; 105:1017-1030. [PMID: 33443635 DOI: 10.1007/s00253-021-11093-5] [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: 10/06/2020] [Revised: 12/19/2020] [Accepted: 01/03/2021] [Indexed: 10/22/2022]
Abstract
In the pharmaceutical industry, nanobodies show promising properties for its application in serotherapy targeting the highly diffusible scorpion toxins. The production of recombinant nanobodies in Escherichia coli has been widely studied in shake flask cultures in rich medium. However, there are no upstream bioprocess studies of nanobody production in defined minimal medium and the effect of the induction temperature on the production kinetics. In this work, the effect of the temperature during the expression of the chimeric bispecific nanobody CH10-12 form, showing high scorpion antivenom potential, was studied in bioreactor cultures of E. coli. High biomass concentrations (25 g cdw/L) were achieved in fed-batch mode, and the expression of the CH10-12 nanobody was induced at temperatures 28, 29, 30, 33, and 37°C with a constant glucose feed. For the bispecific form NbF12-10, the induction was performed at 29°C. Biomass and carbon dioxide yields were reported for each culture phase, and the maintenance coefficient was obtained for each strain. Nanobody production in the CH10-12 strain was higher at low temperatures (lower than 30°C) and declined with the increase of the temperature. At 29°C, the CH10-12, NbF12-10, and WK6 strains were compared. Strains CH10-12 and NbF12-10 had a productivity of 0.052 and 0.021 mg/L/h of nanobody, respectively, after 13 h of induction. The specific productivity of the nanobodies was modeled as a function of the induction temperature and the specific growth rates. Experimental results confirm that low temperatures increase the productivity of the nanobody.Key points• Nanobodies with scorpion antivenom activity produced using two recombinant strains.• Nanobodies production was achieved in fed-batch cultures at different induction temperatures.• Low induction temperatures result in high volumetric productivities of the nanobody CH10-12.
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Bentley WE, Davis RH, Kompala DS. Dynamics of induced CAT expression in E. coli. Biotechnol Bioeng 2010; 38:749-60. [PMID: 18600801 DOI: 10.1002/bit.260380709] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dynamics of chemically induced chloramphenicolaceyl-transferase (CAT) expression are determined in batch cultures of Escherichia coli DH5alphaF'IQ [pKK262-1]. This article is directed towards understanding the coupling of induced cloned-protein synthesis and reduced cell growth which are balanced in the optimal system. Experimental results indicate that the best inducer (IPTG) concentration is near 1.0 mM when added during midexponential growth. Lower concentrations cause only weak induction, whereas higher concentrations cause sufficiently strong induction that cell growth is suppressed. Induction at the onset of the stationary phase results in high expression but is accompanied by stimulated protease activity. Also, cell mass yield is adversely affected by enhanced protein synthesis. A structured metabolic model is shown to predict the responses of instantaneous growth rate and productivity which result from protein overexpression. This model can be employed to predict alternative reactor strategies and operating conditions necessary for the design of efficient bioprocess.
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Affiliation(s)
- W E Bentley
- Department of Chemical Engineering, University of Colorado, Boulder, Colorado 80309-0424, USA
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PATNAIK P. SENSITIVITY OF RECOMBINANT FERMENTATION WITH RUN-AWAY PLASMIDS: A STRUCTURED ANALYSIS OF THE EFFECT OF DILUTION RATE. CHEM ENG COMMUN 2007. [DOI: 10.1080/00986449508936287] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- P.R. PATNAIK
- a Institute of Microbial Technology , P.O. Box 1304, Sector 39-A, Chandigark, 160014, India
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Aucoin MG, McMurray-Beaulieu V, Poulin F, Boivin EB, Chen J, Ardelean FM, Cloutier M, Choi YJ, Miguez CB, Jolicoeur M. Identifying conditions for inducible protein production in E. coli: combining a fed-batch and multiple induction approach. Microb Cell Fact 2006; 5:27. [PMID: 16911799 PMCID: PMC1559716 DOI: 10.1186/1475-2859-5-27] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Accepted: 08/15/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the interest of generating large amounts of recombinant protein, inducible systems have been studied to maximize both the growth of the culture and the production of foreign proteins. Even though thermo-inducible systems were developed in the late 1970's, the number of studies that focus on strategies for the implementation at bioreactor scale is limited. In this work, the bacteriophage lambda PL promoter is once again investigated as an inducible element but for the production of green fluorescent protein (GFP). Culture temperature, induction point, induction duration and number of inductions were considered as factors to maximize GFP production in a 20-L bioreactor. RESULTS It was found that cultures carried out at 37 degrees C resulted in a growth-associated production of GFP without the need of an induction at 42 degrees C. Specific production was similar to what was achieved when separating the growth and production phases. Shake flask cultures were used to screen for desirable operating conditions. It was found that multiple inductions increased the production of GFP. Induction decreased the growth rate and substrate yield coefficients; therefore, two time domains (before and after induction) having different kinetic parameters were created to fit a model to the data collected. CONCLUSION Based on two batch runs and the simulation of culture dynamics, a pre-defined feeding and induction strategy was developed to increase the volumetric yield of a temperature regulated expression system and was successfully implemented in a 20-L bioreactor. An overall cell density of 5.95 g DW l(-1) was achieved without detriment to the cell specific production of GFP; however, the production of GFP was underestimated in the simulations due to a significant contribution of non-growth associated product formation under limiting nutrient conditions.
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Affiliation(s)
- Marc G Aucoin
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montreal, Quebec, Canada
| | - Virginie McMurray-Beaulieu
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Frédéric Poulin
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Eric B Boivin
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Jingkui Chen
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Francisc M Ardelean
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Mathieu Cloutier
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
| | - Young J Choi
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montreal, Quebec, Canada
| | - Carlos B Miguez
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montreal, Quebec, Canada
| | - Mario Jolicoeur
- Canada Research Chair on the Development of Metabolic Engineering Tools, Bio-PResearch Unit, Department of Chemical Engineering, Ecole Polytechnique de Montréal, P.O. Box 6079, Centre-Ville Station Montreal, Quebec, Canada
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Zheng ZY, Yao SJ, Lin DQ. Using a kinetic model that considers cell segregation to optimize hEGF expression in fed-batch cultures of recombinant Escherichia coli. Bioprocess Biosyst Eng 2005; 27:143-52. [PMID: 15806383 DOI: 10.1007/s00449-004-0376-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Accepted: 06/30/2004] [Indexed: 11/29/2022]
Abstract
Growth inhibition of recombinant Escherichia coli during the expression of human epidermal growth factor was observed. The recombinant cells could be segregated into three populations based on their cell division and plasmid maintenance abilities: dividing and plasmid-bearing cells, dividing and plasmid-free cells, and viable-but-non-culturable (VBNC) cells. Fed-batch fermentations were performed to investigate the effect of cell segregation on the kinetics of growth and foreign protein production. The results showed that a low concentration of inducer caused weak induction, whereas high levels cause strong induction, resulting in cells segregating into VBNC bacteria and producing a low foreign protein yield. A kinetic model for cell segregation was proposed and its predictions correlated well with experimental data for cell growth and protein expression. The optimal induction strategy could then be predicted by the model, and this prediction was then verified by experimentally deriving the conditions necessary for maximum expression of recombinant protein.
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Affiliation(s)
- Zhi-Yong Zheng
- Department of Chemical and Biochemical Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
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Modeling of the induced expression for high-level production of a foreign protein by recombinant E. coli under the control of the T7 phage promoter. Process Biochem 2003. [DOI: 10.1016/s0032-9592(03)00077-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Eriksen NT, Kratchmarova I, Neve S, Kristiansen K, Iversen JJ. Automatic inducer addition and harvesting of recombinant Escherichia coli cultures based on indirect on-line estimation of biomass concentration and specific growth rate. Biotechnol Bioeng 2001; 75:355-61. [PMID: 11590608 DOI: 10.1002/bit.10057] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This article describes a novel bioreactor configuration for production optimization of recombinant proteins in Escherichia coli. Inducer addition and harvesting are controlled on-line based on indirect estimation of biomass concentration and specific growth rate from addition of NaOH to maintain constant pH. When either a predetermined biomass concentration is reached or the cultures have obtained, a constant specific growth rate inducer is introduced automatically. The induction period is ended by automatic harvesting of the cultures either at a predetermined biomass concentration or when substrate (in this study glucose) is depleted, detected as an increase of pH, or dissolved oxygen tension. During harvesting, metabolic activities are quenched within 3 min by cooling of the cell suspension. The system has been used to optimize expression of glutathione S-transferase (GST) fusion protein of the ligand binding domain of mouse peroxisome proliferator-activated receptor, GST-PPARalpha LBD. Total yield of GST-PPARalpha LBD was independent of the time of inducer addition as long as the length of induction period corresponded to at least 0.25 cell divisions while the yield of soluble GST-PPARalpha LBD, the only active form, increased with the length of induction period. Highest yields were obtained when the inducer was added at low cell concentration as soon as constant specific growth rate was detected, resulting in induction periods corresponding to 3.4 +/- 0.4 cell divisions. The specific growth rate remained almost constant for one cell division after inducer addition, whereafter it decreased. No decrease of specific growth rate was observed when inducer was added in the lag-phase, and no soluble protein was produced. These results suggest that solely soluble GST-PPARalpha LBD acts as a growth inhibitor and that GST-PPARalpha LBD is expressed predominantly as inclusion bodies immediately after inducer addition whereas the proportion expressed as soluble protein is increased after 1 h of induction. Compared to the procedures, which are generally used for protein expression in the laboratory, this system is less labor intensive, it automatically provides recording of biomass concentration and specific growth rate, and it allows direct comparisons between expression of different proteins and performance of different constructs since the induction period is linked to growth.
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Affiliation(s)
- N T Eriksen
- Department of Biochemistry and Molecular Biology, Odense University Campus, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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Hasty J, McMillen D, Isaacs F, Collins JJ. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet 2001; 2:268-79. [PMID: 11283699 DOI: 10.1038/35066056] [Citation(s) in RCA: 425] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Remarkable progress in genomic research is leading to a complete map of the building blocks of biology. Knowledge of this map is, in turn, setting the stage for a fundamental description of cellular function at the DNA level. Such a description will entail an understanding of gene regulation, in which proteins often regulate their own production or that of other proteins in a complex web of interactions. The implications of the underlying logic of genetic networks are difficult to deduce through experimental techniques alone, and successful approaches will probably involve the union of new experiments and computational modelling techniques.
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Affiliation(s)
- J Hasty
- Centre for BioDynamics and Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, Massachusetts 02215, USA.
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Santillan M, Mackey MC. Dynamic behavior in mathematical models of the tryptophan operon. CHAOS (WOODBURY, N.Y.) 2001; 11:261-268. [PMID: 12779459 DOI: 10.1063/1.1336806] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This paper surveys the general theory of operon regulation as first formulated by Goodwin and Griffith, and then goes on to consider in detail models of regulation of tryptophan production by Bliss, Sinha, and Santillan and Mackey, and the interrelationships between them. We further give a linear stability analysis of the Santillan and Mackey model for wild type E. coli as well as three different mutant strains that have been previously studied in the literature. This stability analysis indicates that the tryptophan production systems should be stable, which is in accord with our numerical results. (c) 2001 American Institute of Physics.
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Affiliation(s)
- Moises Santillan
- Escuela Superior de Fisica y Matematicas, Instituto Politecnico Nacional, 07738, Mexico D.F., Mexico
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Chae HJ, Delisa MP, Cha HJ, Weigand WA, Rao G, Bentley WE. Framework for online optimization of recombinant protein expression in high-cell-density Escherichia coli cultures using GFP-fusion monitoring. Biotechnol Bioeng 2000; 69:275-85. [PMID: 10861407 DOI: 10.1002/1097-0290(20000805)69:3<275::aid-bit5>3.0.co;2-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A framework for the online optimization of protein induction using green fluorescent protein (GFP)-monitoring technology was developed for high-cell-density cultivation of Escherichia coli. A simple and unstructured mathematical model was developed that described well the dynamics of cloned chloramphenicol acetyltransferase (CAT) production in E. coli JM105 was developed. A sequential quadratic programming (SQP) optimization algorithm was used to estimate model parameter values and to solve optimal open-loop control problems for piecewise control of inducer feed rates that maximize productivity. The optimal inducer feeding profile for an arabinose induction system was different from that of an isopropyl-beta-D-thiogalactopyranoside (IPTG) induction system. Also, model-based online parameter estimation and online optimization algorithms were developed to determine optimal inducer feeding rates for eventual use of a feedback signal from a GFP fluorescence probe (direct product monitoring with 95-minute time delay). Because the numerical algorithms required minimal processing time, the potential for product-based and model-based online optimal control methodology can be realized.
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Affiliation(s)
- H J Chae
- Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park 20742, USA
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Donovan RS, Robinson CW, Glick BR. Review: optimizing inducer and culture conditions for expression of foreign proteins under the control of the lac promoter. JOURNAL OF INDUSTRIAL MICROBIOLOGY 1996; 16:145-54. [PMID: 8652113 DOI: 10.1007/bf01569997] [Citation(s) in RCA: 215] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This review examines factors which influence the expression of foreign proteins in Escherichia coli under the transcriptional control of the lac and tac promoters, and discusses conditions for maximizing the production of a foreign protein using this system. Specifically, the influence of IPTG (isopropyl-beta-D-thiogalactoside) concentration, temperature, composition of the growth medium, the point in the growth curve at which cells are induced with either IPTG or lactose, and the duration of the induction phase are discussed.
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Affiliation(s)
- R S Donovan
- Department of Chemical Engineering, University of Waterloo, Ontario, Canada
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Koh BT, Yap MGS. A Simple genetically structured model oftrp repressor-operator interactions. Biotechnol Bioeng 1993; 41:707-14. [DOI: 10.1002/bit.260410705] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Chen W, Bailey JE, Lee SB. Molecular design of expression systems: Comparison of different control configurations using molecular mechanism models. Biotechnol Bioeng 1991; 38:679-87. [DOI: 10.1002/bit.260380702] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Modeling fermentations with recombinant microorganisms: Formulation of a structured model. Biotechnol Bioeng 1991; 37:802-8. [DOI: 10.1002/bit.260370903] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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