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Steimann T, Heite Z, Germer A, Blank LM, Büchs J, Mann M, Magnus JB. Understanding exopolysaccharide byproduct formation in Komagataella phaffii fermentation processes for recombinant protein production. Microb Cell Fact 2024; 23:131. [PMID: 38711081 DOI: 10.1186/s12934-024-02403-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Komagataella phaffii (Pichia pastoris) has emerged as a common and robust biotechnological platform organism, to produce recombinant proteins and other bioproducts of commercial interest. Key advantage of K. phaffii is the secretion of recombinant proteins, coupled with a low host protein secretion. This facilitates downstream processing, resulting in high purity of the target protein. However, a significant but often overlooked aspect is the presence of an unknown polysaccharide impurity in the supernatant. Surprisingly, this impurity has received limited attention in the literature, and its presence and quantification are rarely addressed. RESULTS This study aims to quantify this exopolysaccharide in high cell density recombinant protein production processes and identify its origin. In stirred tank fed-batch fermentations with a maximal cell dry weight of 155 g/L, the polysaccharide concentration in the supernatant can reach up to 8.7 g/L. This level is similar to the achievable target protein concentration. Importantly, the results demonstrate that exopolysaccharide production is independent of the substrate and the protein production process itself. Instead, it is directly correlated with biomass formation and proportional to cell dry weight. Cell lysis can confidently be ruled out as the source of this exopolysaccharide in the culture medium. Furthermore, the polysaccharide secretion can be linked to a mutation in the HOC1 gene, featured by all derivatives of strain NRRL Y-11430, leading to a characteristic thinner cell wall. CONCLUSIONS This research sheds light on a previously disregarded aspect of K. phaffii fermentations, emphasizing the importance of monitoring and addressing the exopolysaccharide impurity in biotechnological applications, independent of the recombinant protein produced.
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Affiliation(s)
- Thomas Steimann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Zoe Heite
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Andrea Germer
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Lars Mathias Blank
- iAMB-Institute of Applied Microbiology, RWTH Aachen University, Worringer Weg 1, 52074, Aachen, Germany
| | - Jochen Büchs
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Marcel Mann
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany
| | - Jørgen Barsett Magnus
- AVT-Biochemical Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074, Aachen, Germany.
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Li H, Chen J, Li X, Gan J, Liu H, Jian Z, Xu S, Zhang A, Li G, Chen K. Artificial neural network and genetic algorithm coupled fermentation kinetics to regulate L-lysine fermentation. BIORESOURCE TECHNOLOGY 2024; 393:130151. [PMID: 38049019 DOI: 10.1016/j.biortech.2023.130151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
Fermentation plays a pivotal role in the industrialization of bioproducts, yet there is a substantial lag in the fermentation process regulation. Here, an artificial neural network (ANN) and genetic algorithm (GA) coupled with fermentation kinetics were employed to establish an innovative lysine fermentation control. Firstly, the strategy of coupling GA with ANN was established. Secondly, specific lysine formation rate (qp), specific substrate consumption rate (qs), and specific cell growth rate (μ) were predicted and optimized by ANN-GA. The optimal ANN model adopts a three-layer feed-forward back-propagation structure (4:10:1). The optimal fermentation control parameters are obtained through GA. Finally, when the carbon to nitrogen ratio, residual sugar concentration, ammonia nitrogen concentration, and dissolved oxygen were [2.5, 4.5], [6.5, 9.5] g·L-1, [1.0, 2.0] g·L-1 and [20, 30] %, respectively, the lysine concentration reaches its peak at 213.0 ± 5.10 g·L-1. The novel control strategy holds significant potential for optimizing the fermentation of other bioproducts.
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Affiliation(s)
- Hui Li
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jiajun Chen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Xingyan Li
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Jian Gan
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Huazong Liu
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Zhou Jian
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Sheng Xu
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Alei Zhang
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China
| | - Ganlu Li
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.
| | - Kequan Chen
- College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211816, China.
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Customized yeast cell factories for biopharmaceuticals: from cell engineering to process scale up. Microb Cell Fact 2021; 20:124. [PMID: 34193127 PMCID: PMC8246677 DOI: 10.1186/s12934-021-01617-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023] Open
Abstract
The manufacture of recombinant therapeutics is a fastest-developing section of therapeutic pharmaceuticals and presently plays a significant role in disease management. Yeasts are established eukaryotic host for heterologous protein production and offer distinctive benefits in synthesising pharmaceutical recombinants. Yeasts are proficient of vigorous growth on inexpensive media, easy for gene manipulations, and are capable of adding post translational changes of eukaryotes. Saccharomyces cerevisiae is model yeast that has been applied as a main host for the manufacture of pharmaceuticals and is the major tool box for genetic studies; nevertheless, numerous other yeasts comprising Pichia pastoris, Kluyveromyces lactis, Hansenula polymorpha, and Yarrowia lipolytica have attained huge attention as non-conventional partners intended for the industrial manufacture of heterologous proteins. Here we review the advances in yeast gene manipulation tools and techniques for heterologous pharmaceutical protein synthesis. Application of secretory pathway engineering, glycosylation engineering strategies and fermentation scale-up strategies in customizing yeast cells for the synthesis of therapeutic proteins has been meticulously described.
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Caballero-Pérez A, Viader-Salvadó JM, Herrera-Estala AL, Fuentes-Garibay JA, Guerrero-Olazarán M. Buried Kex2 Sites in Glargine Precursor Aggregates Prevent Its Intracellular Processing in Pichia pastoris Mut s Strains and the Effect of Methanol-Feeding Strategy and Induction Temperature on Glargine Precursor Production Parameters. Appl Biochem Biotechnol 2021; 193:2806-2829. [PMID: 33931817 DOI: 10.1007/s12010-021-03567-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/08/2021] [Indexed: 11/30/2022]
Abstract
Glargine is a long-acting insulin analog with less hypoglycemia risk. Like human insulin, glargine is a globular protein composed of two polypeptide chains linked by two disulfide bonds. Pichia pastoris KM71 Muts strains were engineered to produce and secrete insulin glargine through the cleavage of two Kex2 sites. Nevertheless, the recombinant product was the single-chain insulin glargine (glargine precursor) instead of the expected double-chain glargine. Molecular model analysis of the dimeric and hexameric forms of the single-chain glargine showed buried Kex2 sites that prevent intracellular glargine precursor processing. The effect of the methanol-feeding strategy (methanol limited fed-batch vs. methanol non-limited fed-batch) and the induction temperature (28 °C vs. 24 °C) on the cell growth and production parameters in bioreactor cultures was also evaluated. Exponential growth at a constant specific growth rate was observed in all the cultures. The volumetric productivities and specific substrate consumption rates were directly proportional to the specific growth rate. The lower temperature led to increased metabolic activity of the yeast cells, which increased the specific growth rate. The methanol non-limited fed-batch culture at 24 °C showed the highest values for the process parameters. After 75 h of induction, 0.122 g/L of glargine precursor was obtained from the culture medium.
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Affiliation(s)
- Abel Caballero-Pérez
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, N.L, Mexico
| | - José María Viader-Salvadó
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, N.L, Mexico
| | - Ana Lucía Herrera-Estala
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, N.L, Mexico
| | - José Antonio Fuentes-Garibay
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, N.L, Mexico
| | - Martha Guerrero-Olazarán
- Instituto de Biotecnología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, UANL, 66455, San Nicolás de los Garza, N.L, Mexico.
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Pekarsky A, Mihalyi S, Weiss M, Limbeck A, Spadiut O. Depletion of Boric Acid and Cobalt from Cultivation Media: Impact on Recombinant Protein Production with Komagataella phaffii. Bioengineering (Basel) 2020; 7:bioengineering7040161. [PMID: 33322107 PMCID: PMC7763993 DOI: 10.3390/bioengineering7040161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 11/23/2022] Open
Abstract
The REACH regulation stands for “Registration, Evaluation, Authorization and Restriction of Chemicals” and defines certain substances as harmful to human health and the environment. This urges manufacturers to adapt production processes. Boric acid and cobalt dichloride represent such harmful ingredients, but are commonly used in yeast cultivation media. The yeast Komagataella phaffii (Pichia pastoris) is an important host for heterologous protein production and compliance with the REACH regulation is desirable. Boric acid and cobalt dichloride are used as boron and cobalt sources, respectively. Boron and cobalt support growth and productivity and a number of cobalt-containing enzymes exist. Therefore, depletion of boric acid and cobalt dichloride could have various negative effects, but knowledge is currently scarce. Herein, we provide an insight into the impact of boric acid and cobalt depletion on recombinant protein production with K. phaffii and additionally show how different vessel materials affect cultivation media compositions through leaking elements. We found that boric acid could be substituted through boron leakiness from borosilicate glassware. Furthermore, depletion of boric acid and cobalt dichloride neither affected high cell density cultivation nor cell morphology and viability on methanol. However, final protein quality of three different industrially relevant enzymes was affected in various ways.
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Affiliation(s)
- Alexander Pekarsky
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Sophia Mihalyi
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
| | - Maximilian Weiss
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Andreas Limbeck
- Institute of Chemical Technologies and Analytics, TU Wien, Getreidemarkt 9/164-I2AC, 1060 Vienna, Austria; (M.W.); (A.L.)
| | - Oliver Spadiut
- Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Gumpendorferstrasse 1a, 1060 Vienna, Austria; (A.P.); (S.M.)
- Correspondence: ; Tel.: +43-1-58801-166473
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Borčinová M, Raschmanová H, Zamora I, Looser V, Marešová H, Hirsch S, Kyslík P, Kovar K. Production and secretion dynamics of prokaryotic Penicillin G acylase in Pichia pastoris. Appl Microbiol Biotechnol 2020; 104:5787-5800. [PMID: 32424437 PMCID: PMC7306039 DOI: 10.1007/s00253-020-10669-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/29/2020] [Accepted: 05/04/2020] [Indexed: 12/13/2022]
Abstract
To take full advantage of recombinant Pichia pastoris (Komagataella phaffii) as a production system for heterologous proteins, the complex protein secretory process should be understood and optimised by circumventing bottlenecks. Typically, little or no attention has been paid to the fate of newly synthesised protein inside the cell, or its passage through the secretory pathway, and only the secreted product is measured. However, the system’s productivity (i.e. specific production rate qp), includes productivity of secreted (qp,extra) plus intracellularly accumulated (qp,intra) protein. In bioreactor cultivations with P. pastoris producing penicillin G acylase, we studied the dynamics of product formation, i.e. both the specific product secretion (qp,extra) and product retention (qp,intra) as functions of time, as well as the kinetics, i.e. productivity in relation to specific growth rate (μ). Within the time course, we distinguished (I) an initial phase with constant productivities, where the majority of product accumulated inside the cells, and qp,extra, which depended on μ in a bell-shaped manner; (II) a transition phase, in which intracellular product accumulation reached a maximum and productivities (intracellular, extracellular, overall) were changing; (III) a new phase with constant productivities, where secretion prevailed over intracellular accumulation, qp,extra was linearly related to μ and was up to three times higher than in initial phase (I), while qp,intra decreased 4–6-fold. We show that stress caused by heterologous protein production induces cellular imbalance leading to a secretory bottleneck that ultimately reaches equilibrium. This understanding may help to develop cultivation strategies for improving protein secretion from P. pastoris.Key Points • A novel concept for industrial bioprocess development. • A Relationship between biomass growth and product formation in P. pastoris. • A Three (3) phases of protein production/secretion controlled by the AOX1-promoter. • A Proof of concept in production of industrially relevant penicillin G acylase. |
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Affiliation(s)
- Martina Borčinová
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Campus Grüental, CH-8820, Wädenswil, Switzerland. .,Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 12840, Prague, Czech Republic.
| | - Hana Raschmanová
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Campus Grüental, CH-8820, Wädenswil, Switzerland.,Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Iwo Zamora
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Campus Grüental, CH-8820, Wädenswil, Switzerland.,Infors AG, Rittergasse 27, CH-4103, Bottmingen, Switzerland
| | - Verena Looser
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Campus Grüental, CH-8820, Wädenswil, Switzerland.,Department of Biotechnology, Faculty of Food and Biochemical Technology, University of Chemistry and Technology, Technická 5, 16628, Prague, Czech Republic
| | - Helena Marešová
- Institute of Microbiology, Czech Academy of Sciences, Videňská 1083, 14220, Prague, Czech Republic
| | - Sven Hirsch
- Institute of Applied Simulation, Zurich University of Applied Sciences, Schloss 1, CH-8820, Wädenswil, Switzerland
| | - Pavel Kyslík
- Institute of Microbiology, Czech Academy of Sciences, Videňská 1083, 14220, Prague, Czech Republic
| | - Karin Kovar
- Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, Campus Grüental, CH-8820, Wädenswil, Switzerland.,Daspool, Gerberacherweg 24, CH-8820, Wädenswil, Switzerland
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Tavasoli T, Arjmand S, Ranaei Siadat SO, Shojaosadati SA, Sahebghadam Lotfi A. A robust feeding control strategy adjusted and optimized by a neural network for enhancing of alpha 1-antitrypsin production in Pichia pastoris. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Effects of glycerol supply and specific growth rate on methanol-free production of CALB by P. pastoris: functional characterisation of a novel promoter. Appl Microbiol Biotechnol 2017; 101:3163-3176. [PMID: 28130631 PMCID: PMC5380701 DOI: 10.1007/s00253-017-8123-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/03/2017] [Accepted: 01/10/2017] [Indexed: 12/20/2022]
Abstract
As Pichia pastoris (syn. Komagataella sp.) yeast can secrete pure recombinant proteins at high rates, it is a desirable production system. The function of a novel synthetic variant of the AOX1 promoter was characterised comprehensively using a strain secreting Candida antarctica lipase B (CALB) as a model. A new time-saving approach was introduced to determine, in only one experiment, the hitherto unknown relationship between specific product formation rate (qp) and specific growth rate (μ). Tight control of recombinant protein formation was possible in the absence of methanol, while using glycerol as a sole carbon/energy source. CALB was not synthesised during batch cultivation in excess glycerol (>10 g l−1) and at a growth rate close to μmax (0.15 h−1). Between 0.017 and 0.115 h−1 in glycerol-limited fedbatch cultures, basal levels of qp > 0.4 mg g−1 h−1 CALB were reached, independent of the μ at which the culture grew. At μ > 0.04 h−1, an elevated qp occurred temporarily during the first 20 h after changing to fedbatch mode and decreased thereafter to basal. In order to accelerate the determination of the qp(μ) relationship (kinetics of product formation), the entire μ range was covered in a single fedbatch experiment. By linearly increasing and decreasing glycerol addition rates, μ values were repeatedly shifted from 0.004 to 0.074 h−1 and vice versa. Changes in qp were related to changes in μ. A rough estimation of μ range suitable for production was possible in a single fedbatch, thus significantly reducing the experimental input over previous approaches comprising several experiments.
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Looser V, Bruhlmann B, Bumbak F, Stenger C, Costa M, Camattari A, Fotiadis D, Kovar K. Cultivation strategies to enhance productivity of Pichia pastoris: A review. Biotechnol Adv 2015; 33:1177-93. [DOI: 10.1016/j.biotechadv.2015.05.008] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 05/11/2015] [Accepted: 05/25/2015] [Indexed: 12/14/2022]
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Potvin G, Ahmad A, Zhang Z. Bioprocess engineering aspects of heterologous protein production in Pichia pastoris: A review. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2010.07.017] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Use of a mixture of glucose and methanol as substrates for the production of recombinant trypsinogen in continuous cultures with Pichia pastoris Mut+. J Biotechnol 2012; 157:180-8. [DOI: 10.1016/j.jbiotec.2011.10.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 10/10/2011] [Accepted: 10/27/2011] [Indexed: 11/19/2022]
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Improvement of ATP regeneration efficiency and operation stability in porcine interferon-α production by Pichia pastoris under lower induction temperature. KOREAN J CHEM ENG 2011. [DOI: 10.1007/s11814-010-0527-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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