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Guez JS, Lacroix PY, Château T, Vial C. Deep in situ microscopy for real-time analysis of mammalian cell populations in bioreactors. Sci Rep 2023; 13:22045. [PMID: 38086908 PMCID: PMC10716407 DOI: 10.1038/s41598-023-48733-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
An in situ microscope based on pulsed transmitted light illumination via optical fiber was combined to artificial-intelligence to enable for the first time an online cell classification according to well-known cellular morphological features. A 848 192-image database generated during a lab-scale production process of antibodies was processed using a convolutional neural network approach chosen for its accurate real-time object detection capabilities. In order to induce different cell death routes, hybridomas were grown in normal or suboptimal conditions in a stirred tank reactor, in the presence of substrate limitation, medium addition, pH regulation problem or oxygen depletion. Using such an optical system made it possible to monitor real-time the evolution of different classes of animal cells, among which viable, necrotic and apoptotic cells. A class of viable cells displaying bulges in feast or famine conditions was also revealed. Considered as a breakthrough in the catalogue of process analytical tools, in situ microscopy powered by artificial-intelligence is also of great interest for research.
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Affiliation(s)
- Jean-Sébastien Guez
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, 63 000, Clermont-Ferrand, France.
| | - Pierre-Yves Lacroix
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, 63 000, Clermont-Ferrand, France
- Logiroad.AI, 63 178, Aubière, France
| | - Thierry Château
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, 63 000, Clermont-Ferrand, France
- Logiroad.AI, 63 178, Aubière, France
| | - Christophe Vial
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, 63 000, Clermont-Ferrand, France
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Guez JS, Coucheney F, Guy J, Béchet M, Fontanille P, Chihib NE, Niehren J, Coutte F, Jacques P. Bioinformatics Modelling and Metabolic Engineering of the Branched Chain Amino Acid Pathway for Specific Production of Mycosubtilin Isoforms in Bacillus subtilis. Metabolites 2022; 12:metabo12020107. [PMID: 35208182 PMCID: PMC8877110 DOI: 10.3390/metabo12020107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
Mycosubtilin belongs to the family of lipopeptides. Different isoforms with various antifungal activities can be obtained according to the length and the isomery of the fatty acid. In this work, the activities of the mycosubtilin isoforms were first studied against the pathogen Aspergillus niger, revealing the high activity of the anteiso-C17 isoform. Modification of the mycosubtilin isoform patterns during cultures of the natural strain Bacillus subtilis ATCC 6633 was then investigated through amino acid feeding experiments. In parallel, single-gene knockouts and single-gene overexpression, leading to the overproduction of the anteiso-C15 fatty acid chains, were predicted using informatics tools which provide logical reasoning with formal models of reaction networks. In this way, it was in silico predicted that the single overexpression of the ilvA gene as well as the single knockout of the codY gene may lead to the overproduction of anteiso-C15 fatty acid chains. For the first time, it has been demonstrated that overexpression of ilvA helps to enhance the furniture of odd anteiso fatty acids leading to a favored mycosubtilin anteiso-C17 production pattern (+41%). Alternatively, a knock-out codY mutant led to a higher furniture of even iso fatty acids, leading to a favored mycosubtilin iso-C16 production pattern (+180%). These results showed that increased selective synthesis of particular isoforms of mycosubtilin through metabolic engineering is feasible, disclosing the interest of these approaches for future development of lipopeptide-producing strains.
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Affiliation(s)
- Jean-Sébastien Guez
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Françoise Coucheney
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Joany Guy
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Max Béchet
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
| | - Pierre Fontanille
- Institut Pascal, Clermont Auvergne INP, CNRS, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France; (J.-S.G.); (P.F.)
| | - Nour-Eddine Chihib
- UMR 8207–UMET–Unité Matériaux et Transformations, Centrale Lille, INRAE, CNRS, Université de Lille, F-59000 Lille, France;
| | - Joachim Niehren
- Biocomputing Team, Centre de Recherche en Informatique, Signal et Automatique de Lille CRIStAL, UMR CNRS 9189, Université de Lille, F-59000 Lille, France;
- INRIA, Université de Lille, F-59000 Lille, France
| | - François Coutte
- Équipe Métabolites Secondaires d’Origine Microbienne, Institut Charles Viollette, UMRt BioEcoAgro 1158-INRAE, Université de Lille, F-59000 Lille, France; (F.C.); (J.G.); (M.B.)
- Correspondence: ; Tel.: +33-(0)-328767497
| | - Philippe Jacques
- Équipe Métabolites Spécialisés d’Origine Microbienne, UMRt BioEcoAgro 1158-INRAE, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Université de Liège, B-5030 Gembloux, Belgium;
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Guez JS, Vassaux A, Larroche C, Jacques P, Coutte F. New Continuous Process for the Production of Lipopeptide Biosurfactants in Foam Overflowing Bioreactor. Front Bioeng Biotechnol 2021; 9:678469. [PMID: 34124025 PMCID: PMC8194703 DOI: 10.3389/fbioe.2021.678469] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
In this work, an original culture process in bioreactor named overflowing continuous culture (O-CC) was developed to produce and recover continuously mycosubtilin, a lipopeptide antifungal biosurfactant of major interest. The lipopeptide production was first investigated in shake conical flasks in different culture media [ammonium citrate sucrose (ACS), Difco sporulation medium (DSM), and Landy], followed by a pH condition optimization using 3-(N-morpholino)propanesulfonic acid (MOPS) and 2-(N-morpholino)ethanesulfonic acid (MES) buffered media. A simple theoretical modeling of the biomass evolution combined with an experimental setup was then proposed for O-CC processed in stirred tank reactor at laboratory scale. Seven O-CC experiments were done in modified Landy medium at the optimized pH 6.5 by applying dilution rates comprised between 0.05 and 0.1 h-1. The O-CC allowed the continuous recovery of the mycosubtilin contained in the foam overflowing out of the reactor, achieving a remarkable in situ product removal superior to 99%. The biomass concentration in the overflowing foam was found to be twofold lower than the biomass concentration in the reactor, relating advantageously this process to a continuous one with biomass feedback. To evaluate its performances regarding the type of lipopeptide produced, the O-CC process was tested with strain BBG116, a mycosubtilin constitutive overproducing strain that also produces surfactin, and strain BBG125, its derivative strain obtained by deleting surfactin synthetase operon. At a dilution rate of 0.1 h-1, specific productivity of 1.18 mg of mycosubtilin⋅g-1(DW)⋅h-1 was reached. Compared with other previously described bioprocesses using almost similar culture conditions and strains, the O-CC one allowed an increase of the mycosubtilin production rate by 2.06-fold.
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Affiliation(s)
- Jean-Sébastien Guez
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, Clermont-Ferrand, France
| | - Antoine Vassaux
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, Institut Charles Viollette, Lille, France
| | - Christian Larroche
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, Clermont-Ferrand, France
| | - Philippe Jacques
- Université de Liège, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, TERRA Teaching and Research Centre, MiPI, Gembloux Agro-Bio Tech, Gembloux, Belgium.,Lipofabrik, Polytech-Lille, Cité Scientifique, Villeneuve d'Ascq, France
| | - François Coutte
- Université de Lille, UMRt BioEcoAgro 1158-INRAE, équipe Métabolites Secondaires d'origine Microbienne, Institut Charles Viollette, Lille, France.,Lipofabrik, Polytech-Lille, Cité Scientifique, Villeneuve d'Ascq, France
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Coutte F, Lecouturier D, Dimitrov K, Guez JS, Delvigne F, Dhulster P, Jacques P. Microbial lipopeptide production and purification bioprocesses, current progress and future challenges. Biotechnol J 2017. [DOI: 10.1002/biot.201600566] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- François Coutte
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Didier Lecouturier
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Krasimir Dimitrov
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Jean-Sébastien Guez
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
- Axe GePEB, Institut Pascal, UMR 6602; Université Clermont Auvergne, CNRS, SIGMA; Clermont-Ferrand France
| | - Frank Delvigne
- Microbial Processes and Interactions, TERRA Teaching and Research Centre; Gembloux Agro-Bio Tech University of Liege; Gembloux Belgium
| | - Pascal Dhulster
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
| | - Philippe Jacques
- Institut Charles Viollette, Université Lille, INRA, ISA, Université d'Artois; Université Littoral Côte d'Opale; EA 7394-ICV Lille France
- Microbial Processes and Interactions, TERRA Teaching and Research Centre; Gembloux Agro-Bio Tech University of Liege; Gembloux Belgium
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Béchet M, Castéra-Guy J, Guez JS, Chihib NE, Coucheney F, Coutte F, Fickers P, Leclère V, Wathelet B, Jacques P. Production of a novel mixture of mycosubtilins by mutants of Bacillus subtilis. Bioresour Technol 2013; 145:264-270. [PMID: 23583475 DOI: 10.1016/j.biortech.2013.03.123] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 03/13/2013] [Accepted: 03/15/2013] [Indexed: 06/02/2023]
Abstract
Using promoter exchange and gene knock-out strategies, two mutant strains, the so-called BBG116 and BBG125, were constructed from Bacillus subtilis wild-type strain ATCC 6633, a surfactin and mycosubtilin producer. Compared to the parental strain, both mutants overproduced constitutively mycosubtilin, while BBG125 had lost the ability to synthesize surfactin. Surprisingly, BBG125 was found to produce about 2-fold less mycosubtilin than BBG116 despite an expected higher availability of the cytoplasmic precursors and cofactors pool for biosynthesis. Further physiological characterization of BBG125 also highlighted: (i) a strong influence of temperature on mycosubtilin biosynthesis in BBG125 with a maximal productivity observed at 22°C, compared to 15 and 30°C; (ii) substantial changes in fatty acid profiles and thereby in mycosubtilin isoforms, compared to the wild-type strain; and (iii) the presence of five novel mycosubtilin isoforms. The antifungal activities of the new mix were higher than or equal to those of purified isoforms.
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Affiliation(s)
- Max Béchet
- Laboratoire des Procédés Biologiques, Génie Enzymatique et Microbien-ProBioGEM, UPRES-EA 1026, Polytech'Lille/IUT A, Université Lille Nord de France-Sciences et Technologies, Villeneuve d'Ascq, France
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Guez JS, Coutte F, Drucbert AS, Chihib NE, Danzé PM, Jacques P. Resistance of the cell wall to degradation is a critical parameter for isolation of high quality RNA from natural isolates of Bacillus subtilis. Arch Microbiol 2009; 191:669-73. [PMID: 19521677 DOI: 10.1007/s00203-009-0487-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 05/25/2009] [Indexed: 11/30/2022]
Abstract
Natural isolates of Bacillus subtilis are known for their ability to produce a large panel of bioactive compounds. Unfortunately, their recalcitrance to conventional molecular techniques limits their transcript studies. In this work, difficulties to isolate RNA attributed to the cell wall were overcome, finally authorising powerful RT-PCR's.
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Affiliation(s)
- Jean-Sébastien Guez
- Laboratoire ProBioGEM, UPRES-EA 1026, Polytech-Lille, IUT A, Université des Sciences et Technologies de Lille, Bd Paul Langevin, 59655, Villeneuve d'Ascq, France.
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Fickers P, Leclère V, Guez JS, Béchet M, Coucheney F, Joris B, Jacques P. Temperature dependence of mycosubtilin homologue production in Bacillus subtilis ATCC6633. Res Microbiol 2008; 159:449-57. [PMID: 18656330 DOI: 10.1016/j.resmic.2008.05.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2008] [Revised: 05/20/2008] [Accepted: 05/20/2008] [Indexed: 11/27/2022]
Abstract
Bacillus subtilis ATCC6633 produces mycosubtilin, a non-ribosomally synthesized lipopeptide of the iturin family which presents antagonistic activities toward various phytopathogens. Different homologues with fatty acid moiety varying from C15 to C17 are usually co-produced, with their biological activities increasing with the number of carbons in the fatty acid chain. In the present report, we highlight that growth temperature modulates both the extent of mycosubtilin production and the relative abundance of the different homologues. A 30-fold increase in mycosubtilin production was observed when the temperature was decreased from 37 degrees C to 25 degrees C for both strain ATCC6633 and its derivative BBG100, a constitutive mycosubtilin overproducer. However, no significant difference in either the expression of the mycosubtilin synthetase encoding genes or in the intracellular synthetase concentration could be found, suggesting that the observed phenotype originated from a higher mycosubtilin synthetase turnover at lower temperature. We also point out that lower growth temperature leads to an increased proportion of odd-numbered fatty acid homologues as a consequence of de novo synthesis of C17 anteiso fatty acid following cell adaptation to low temperatures.
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Affiliation(s)
- Patrick Fickers
- Laboratoire de Procédés biologiques, Génie enzymatique et microbien (ProBioGEM, UPRES EA 1026), Polytech'Lille, Université des Sciences et Technologies de Lille, F-59655 Villeneuve d'Ascq Cedex, France
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Guez JS, Chenikher S, Cassar JP, Jacques P. Setting up and modelling of overflowing fed-batch cultures of Bacillus subtilis for the production and continuous removal of lipopeptides. J Biotechnol 2007; 131:67-75. [PMID: 17624460 DOI: 10.1016/j.jbiotec.2007.05.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 05/11/2007] [Accepted: 05/21/2007] [Indexed: 11/24/2022]
Abstract
This work is related to the set-up of overflowing exponential fed-batch cultures (O-EFBC) derived from carbon limited EFBC dedicated to the production of mycosubtilin, an antifungal lipopeptide belonging to the iturin family. O-EFBC permits the continuous removal of the product from the bioreactor achieving a complete extraction of mycosubtilin. This paper also provides a dynamical Monod-based growth model of this process that is accurate enough to simulate the evolution of the specific growth rate and to correlate it to the mycosubtilin specific productivity. Two particular and dependant phenomena related to the foam overflow are taken into account by the model: the outgoing flow rate of a broth volume and the loss of biomass. Interestingly, the biomass concentration in the foam was found to be lower than the biomass concentration in the bioreactor relating this process to a recycling one. Parameters of this model are the growth yield on substrate and the maximal specific growth rate estimated from experiments led at feed rates of 0.062, 0.071 and 0.086h(-1). The model was extrapolated to five additional experiments carried out at feed rates of 0.008, 0.022, 0.040, 0.042 and 0.062h(-1) enabling the correlation of the mean specific growth rates with productivity results. Finally, a feed rate of 0.086h(-1) corresponding to a mean specific growth rate of 0.070h(-1) allowed a specific productivity of 1.27mg of mycosubtiling(-1) of dried biomassh(-1).
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Affiliation(s)
- J S Guez
- ProBioGEM, Laboratoire des Procédés Biologiques Génie Enzymatique et Microbien, UPRES-EA 1026, Polytech-Lille, Université des Sciences et Technologies de Lille, Bd Paul Langevin, Villeneuve d'Ascq, France.
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Leclère V, Béchet M, Adam A, Guez JS, Wathelet B, Ongena M, Thonart P, Gancel F, Chollet-Imbert M, Jacques P. Mycosubtilin overproduction by Bacillus subtilis BBG100 enhances the organism's antagonistic and biocontrol activities. Appl Environ Microbiol 2005; 71:4577-84. [PMID: 16085851 PMCID: PMC1183317 DOI: 10.1128/aem.71.8.4577-4584.2005] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A Bacillus subtilis derivative was obtained from strain ATCC 6633 by replacement of the native promoter of the mycosubtilin operon by a constitutive promoter originating from the replication gene repU of the Staphylococcus aureus plasmid pUB110. The recombinant strain, designated BBG100, produced up to 15-fold more mycosubtilin than the wild type produced. The overproducing phenotype was related to enhancement of the antagonistic activities against several yeasts and pathogenic fungi. Hemolytic activities were also clearly increased in the modified strain. Mass spectrometry analyses of enriched mycosubtilin extracts showed similar patterns of lipopeptides for BBG100 and the wild type. Interestingly, these analyses also revealed a new form of mycosubtilin which was more easily detected in the BBG100 sample. When tested for its biocontrol potential, wild-type strain ATCC 6633 was almost ineffective for reducing a Pythium infection of tomato seedlings. However, treatment of seeds with the BBG100 overproducing strain resulted in a marked increase in the germination rate of seeds. This protective effect afforded by mycosubtilin overproduction was also visualized by the significantly greater fresh weight of emerging seedlings treated with BBG100 compared to controls or seedlings inoculated with the wild-type strain.
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Affiliation(s)
- Valérie Leclère
- Laboratory of Microbial Bioprocesses (LABEM), Polytech'Lille, University of Science and Technology of Lille, Avenue du Professeur Langevin, F-59655 Villeneuve d'Ascq Cedex, France
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Guez JS, Cassar JP, Wartelle F, Dhulster P, Suhr H. Real time in situ microscopy for animal cell-concentration monitoring during high density culture in bioreactor. J Biotechnol 2004; 111:335-43. [PMID: 15246669 DOI: 10.1016/j.jbiotec.2004.04.028] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 04/26/2004] [Accepted: 04/30/2004] [Indexed: 12/01/2022]
Abstract
An in situ microscope (ISM) device is utilised in this study to monitor hybridoma cells concentration in a stirred bioreactor. It generates images by using pulsed illumination of the liquid broth synchronised with the camera frame generation to avoid blur from the cell's motion. An appropriate image processing isolates the sharp objects from the blurred ones that are far from the focal plane. As image processing involves several parameters, this paper focuses on the robustness of the results of the cells counting. This stage determines the applicability of the measuring device and has seldom been tackled in the presentations of ISM devices. Calibration is secondly performed for assessing the cell-concentration from the cell automated numeration provided by the ISM. Flow cytometry and hemacytometer chamber were used as reference analytical methods. These measures and the output of the image processing allow estimating a single calibration parameter: the reference volume per image equal to 1.08 x 10(-6) mL. In these conditions, the correlation coefficient between both reference and ISM data sets becomes equal to 0.99. A saturation of this system during an ultrasonic wave perfusion phase that deeply changes the culture conditions is observed and discussed. Principal component analysis (PCA) is used to undergo the robustness study and the ISM calibration step.
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Affiliation(s)
- J S Guez
- Laboratoire Génie Biologique et d'Automatique, EPU USTL Lille, 59655 Villeneuve d'Ascq Cedex, France.
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