Jean-louis Uribelarrea | INSA Toulouse (original) (raw)
Papers by Jean-louis Uribelarrea
Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les biopr... more Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les bioprocds pour confirmer et enrichir la connaissance d'expert. Pour cela nous proposons une mthode de clustering base sur la dtection et la slection de singularits par l'exposant de Hölderà partir des coefficients de la Tranforme en Ondelettes.
20° Colloque sur le traitement du signal et des images, FRA, 2005, 2005
Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les biopr... more Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les bioprocds pour confirmer et enrichir la connaissance d'expert. Pour cela nous proposons une mthode de clustering base sur la dtection et la slection de singularits par l'exposant de Hôlder à partir des coefficients de la Tranforme en Ondelettes.
Bioresource Technology, 2015
In a waste into resource strategy, a selection of polyhydroxybutyrate (PHB)-accumulating organism... more In a waste into resource strategy, a selection of polyhydroxybutyrate (PHB)-accumulating organisms from activated sludge was achieved in an open continuous culture under acetic acid and phosphorus limitation. Once the microbial population was selected at a dilution rate (D), an increase in phosphorus limitation degree was applied in order to study the intracellular phosphorus plasticity of selected bacteria and the resulting capacity to produce PHB. Whatever D, all selected populations were able to produce PHB. At a D, the phosphorus availability determined the phosphorus-cell content which in turn fixed the amount of cell. All the remaining carbon was thus directed toward PHB. By decreasing D, microorganisms adapted more easily to higher phosphorus limitation leading to higher PHB content. A one-stage continuous reactor operated at D=0.023h(-)(1) gave reliable high PHB productivity with PHB content up to 80%. A two-stage reactor could ensure better productivity while allowing tuning product quality.
Exopolysaccharide (EPS) was produced by Klebsiella pneumoniae K63 grown in fed-batch cultures usi... more Exopolysaccharide (EPS) was produced by Klebsiella pneumoniae K63 grown in fed-batch cultures using different procedures of the supply of carbon or nitrogen (N) source, or both. Cultures grown with excess of glucose and limitation or exhaustion of N produced 54.8 and 47.4 g EPS l −1 , respectively. These cultures also led to an accumulation of 'overflow' metabolites representing more than 16% of carbon conversion. The consistency indexes (K) obtained to the end of the cultures, characteristic of the rheological property of the biopolymer, were 16.4 Pa s n for N deficiency and 5.2 Pa s n for N limitation conditions. The simultaneous limitation of glucose and N decreased the excretion of co-metabolites (6.4% of carbon conversion) and the EPS production (18.1 g EPS l −1 ), while improving the quality of the polysaccharide, characterized by the highest K of 126.2 Pa s n and the highest pseudoplasticity degree (flow behaviour index, n = 0.2).
Cellular cultures require an in-depth knowledge of biological and physical parameters to control ... more Cellular cultures require an in-depth knowledge of biological and physical parameters to control and optimize the process. Among the physical parameters, viscosity and rheological behaviour are of first importance. This study describes implementation and results obtained with an experimental on-line rheological device mounted on a bioreactor. Description of the set-up and experimental calibration with well-defined Newtonian fluids are presented. An example of a cellular culture (E. coli) is then proposed enlightening the influence of biological activity on rheological behaviour and the need for on-line measurement.
Applied and Environmental Microbiology
During batch growth of Alcaligenes eutrophus on benzoate-plus-succinate mixtures, substrates were... more During batch growth of Alcaligenes eutrophus on benzoate-plus-succinate mixtures, substrates were simultaneously metabolized, leading to a higher specific growth rate ( ؍ 0.56 h ؊1 ) than when a single substrate was used ( ؍ 0.51 h ؊1 for benzoate alone and 0.44 h ؊1 for succinate alone), without adversely affecting the growth yield (0.57 Cmol/Cmol). Flux distribution analysis revealed that succinate dehydrogenase most probably controls the rate of total succinate consumption (the maximum flux being 9.7 mmol ⅐ g ؊1 ⅐ h ؊1 ). It is postulated that the relative consumption rate of each substrate is in part related to modified levels of gene expression but to a large extent is dependent upon the presence of succinate, end product of the -ketoadipate pathway. Indeed, the in vitro -ketoadipate-succinyl coenzyme A transferase activity was seen to be inhibited by succinate, a coproduct of the reaction.
Microorganisms, 2015
Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great int... more Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h(-1) at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h(-1) and D. geothermalis DSM-11302 biomass reached 1.4 g·L(-1) in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc(-1); cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX(-1)·h(-1), respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture.
Biotechnology, Agronomy, Society and Environment
Heterogeneities caused by deficient mixing in large-scale bioreactors have been identified and de... more Heterogeneities caused by deficient mixing in large-scale bioreactors have been identified and described in literature. These heterogeneities affect physiological changes of microorganisms through its passage in different zones of concentrations. Consequently the differences in terms of productivities, qualities and/or yields of products of interest have been observed during scaling-up from laboratory to larger scales. For this reason, large-scale process improvement depends on the understanding of dynamic interactions between microbial responses and physical phenomena inside bioreactors. The dynamic responses of microorganisms are used as a tool for gaining insight into the fundamentals of microbial changes under a mixing-well controlled environment. Our research group has not only applied scale-down methodology to study the microbial responses at molecular, microscopic and macroscopic levels of observation, but also has used innovative strains and process engineering tools to eval...
Enrichment of the medium with yeast extract (20 g.l ) and Tryptone (40 g.l ) increased the growth... more Enrichment of the medium with yeast extract (20 g.l ) and Tryptone (40 g.l ) increased the growth of Lactobacillus casei ssp. rhamnosusand its production of lactic acid in both batch and cell-recycle cultures without affecting glucose consumption and the lactic acid production rate.
Process Biochemistry, 2014
Carbon dioxide (CO 2 ) is a major compound of microbial metabolism both as a substrate and as a p... more Carbon dioxide (CO 2 ) is a major compound of microbial metabolism both as a substrate and as a product but high dissolved carbon dioxide concentrations have long been known to affect yeast physiology.
Extremophiles, 2014
Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have be... more Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have been conducted to date. Three defined media compositions have been published for the growth of this strain but they were found to be inadequate to achieve growth without limitation. Furthermore, growth curves, biomass concentration and growth rates were generally not available. Analysis in Principal Components was used in this work to compare and consequently to highlight the main compounds which differ between published chemically defined media. When available, biomass concentration, and/or growth rate were superimposed to the PCA analysis. The formulations of the media were collected from existing literature; media compositions designed for the growth of several strains of Deinococcaceae or Micrococcaceae were included. The results showed that a defined medium adapted from Holland et al. (Appl Microbiol Biotechnol 72:1074-1082, 2006) was the best basal medium and was chosen for further studies. A growth rate of 0.03 h(-1) and a final OD600nm of 0.55 were obtained, but the growth was linear. Then, the effects of several medium components on oxygen uptake and biomass production by Deinococcus geothermalis DSM 11300 were studied using a respirometry-based method, to search for the nutritional limitation. The results revealed that the whole yeast extract in the medium with glucose is necessary to obtain a non-limiting growth of Deinococcus geothermalis DSM 11300 at a maximum growth rate of 0.64 h(-1) at 45 °C.
Mathematics and Computers in Simulation, 2004
We present modelling software developed under MATLAB in which parameter estimations are obtained ... more We present modelling software developed under MATLAB in which parameter estimations are obtained by using non-linear regression techniques. The different parameters appear in a set of non-linear algebraic and differential equations representing the model of the process. From experimental data obtained in discontinuous cultures a representative mathematical model (unstructured kinetic model) of the macroscopic behaviour of Lactobacillus acidophilus has been developed. An unstructured model expressed the specific rates of cell growth, lactic acid production and glucose consumption for batch fermentation. The model is formulated by considering the inhibition of growth under sub-optimal culture conditions during Lactobacillus acidophilus fermentation, which is accompanied by an increase of the maintenance energy. This study permits to predict the cellular behaviour at low growth temperatures and enables to define the response of the strain to sub-optimal temperature stress.
Journal of Chromatography A, 2011
Response surface methodology (RSM) was used for the determination of optimum extraction parameter... more Response surface methodology (RSM) was used for the determination of optimum extraction parameters to reach maximum lipid extraction yield with yeast. Total lipids were extracted from oleaginous yeast (Rhodotorula glutinis) using pressurized liquid extraction (PLE). The effects of extraction parameters on lipid extraction yield were studied by employing a second-order central composite design. The optimal condition was obtained as three cycles of 15 min at 100 • C with a ratio of 144 g of hydromatrix per 100 g of dry cell weight. Different analysis methods were used to compare the optimized PLE method with two conventional methods (Soxhlet and modification of Bligh and Dyer methods) under efficiency, selectivity and reproducibility criteria thanks to gravimetric analysis, GC with flame ionization detector, High Performance Liquid Chromatography linked to Evaporative Light Scattering Detector (HPLC-ELSD) and thin-layer chromatographic analysis. For each sample, the lipid extraction yield with optimized PLE was higher than those obtained with referenced methods (Soxhlet and Bligh and Dyer methods with, respectively, a recovery of 78% and 85% compared to PLE method). Moreover, the use of PLE led to major advantages such as an analysis time reduction by a factor of 10 and solvent quantity reduction by 70%, compared with traditional extraction methods.
International Journal of Modelling, Identification and Control, 2008
... Carine Bideaux,* Gérard Goma and Jean-Louis Uribelarrea Université de Toulouse, INSA, UPS, IN... more ... Carine Bideaux,* Gérard Goma and Jean-Louis Uribelarrea Université de Toulouse, INSA, UPS, INP; LISBP, I135 Avenue de Rangueil, Toulouse F-31077, France ... Jean-Louis Uribelarrea received his PhD in Microbial Engineering from INSA Toulouse, France, in July 1980. ...
Enzyme and Microbial Technology, 2002
Three inducible and extracellular activities produced by Bacillus subtilis NCIMB 11871 and 11872 ... more Three inducible and extracellular activities produced by Bacillus subtilis NCIMB 11871 and 11872 were identified: a fructosyl transferase, a sucrase and a polymerase activity synthesising fructose polymers. These polymers are responsible for a limitation in the oxygen transfer, probably by increasing the viscosity of the culture medium, and for an opalescent supernatant observed at the end of the exponential growth phase. The production and degradation of the three enzymatic activities was tightly coupled during the time course of micro-organism cultivation. Furthermore, no separation of them was achieved by ammonium sulphate precipitation, ultrafiltration and other separation techniques. We suggest that these three activities are supported by the same enzyme, and that this enzyme is a levansucrase.
Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les biopr... more Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les bioprocds pour confirmer et enrichir la connaissance d'expert. Pour cela nous proposons une mthode de clustering base sur la dtection et la slection de singularits par l'exposant de Hölderà partir des coefficients de la Tranforme en Ondelettes.
20° Colloque sur le traitement du signal et des images, FRA, 2005, 2005
Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les biopr... more Nous cherchons une mthode non supervise qui puisse dtecter des tats physiologiques dans les bioprocds pour confirmer et enrichir la connaissance d'expert. Pour cela nous proposons une mthode de clustering base sur la dtection et la slection de singularits par l'exposant de Hôlder à partir des coefficients de la Tranforme en Ondelettes.
Bioresource Technology, 2015
In a waste into resource strategy, a selection of polyhydroxybutyrate (PHB)-accumulating organism... more In a waste into resource strategy, a selection of polyhydroxybutyrate (PHB)-accumulating organisms from activated sludge was achieved in an open continuous culture under acetic acid and phosphorus limitation. Once the microbial population was selected at a dilution rate (D), an increase in phosphorus limitation degree was applied in order to study the intracellular phosphorus plasticity of selected bacteria and the resulting capacity to produce PHB. Whatever D, all selected populations were able to produce PHB. At a D, the phosphorus availability determined the phosphorus-cell content which in turn fixed the amount of cell. All the remaining carbon was thus directed toward PHB. By decreasing D, microorganisms adapted more easily to higher phosphorus limitation leading to higher PHB content. A one-stage continuous reactor operated at D=0.023h(-)(1) gave reliable high PHB productivity with PHB content up to 80%. A two-stage reactor could ensure better productivity while allowing tuning product quality.
Exopolysaccharide (EPS) was produced by Klebsiella pneumoniae K63 grown in fed-batch cultures usi... more Exopolysaccharide (EPS) was produced by Klebsiella pneumoniae K63 grown in fed-batch cultures using different procedures of the supply of carbon or nitrogen (N) source, or both. Cultures grown with excess of glucose and limitation or exhaustion of N produced 54.8 and 47.4 g EPS l −1 , respectively. These cultures also led to an accumulation of 'overflow' metabolites representing more than 16% of carbon conversion. The consistency indexes (K) obtained to the end of the cultures, characteristic of the rheological property of the biopolymer, were 16.4 Pa s n for N deficiency and 5.2 Pa s n for N limitation conditions. The simultaneous limitation of glucose and N decreased the excretion of co-metabolites (6.4% of carbon conversion) and the EPS production (18.1 g EPS l −1 ), while improving the quality of the polysaccharide, characterized by the highest K of 126.2 Pa s n and the highest pseudoplasticity degree (flow behaviour index, n = 0.2).
Cellular cultures require an in-depth knowledge of biological and physical parameters to control ... more Cellular cultures require an in-depth knowledge of biological and physical parameters to control and optimize the process. Among the physical parameters, viscosity and rheological behaviour are of first importance. This study describes implementation and results obtained with an experimental on-line rheological device mounted on a bioreactor. Description of the set-up and experimental calibration with well-defined Newtonian fluids are presented. An example of a cellular culture (E. coli) is then proposed enlightening the influence of biological activity on rheological behaviour and the need for on-line measurement.
Applied and Environmental Microbiology
During batch growth of Alcaligenes eutrophus on benzoate-plus-succinate mixtures, substrates were... more During batch growth of Alcaligenes eutrophus on benzoate-plus-succinate mixtures, substrates were simultaneously metabolized, leading to a higher specific growth rate ( ؍ 0.56 h ؊1 ) than when a single substrate was used ( ؍ 0.51 h ؊1 for benzoate alone and 0.44 h ؊1 for succinate alone), without adversely affecting the growth yield (0.57 Cmol/Cmol). Flux distribution analysis revealed that succinate dehydrogenase most probably controls the rate of total succinate consumption (the maximum flux being 9.7 mmol ⅐ g ؊1 ⅐ h ؊1 ). It is postulated that the relative consumption rate of each substrate is in part related to modified levels of gene expression but to a large extent is dependent upon the presence of succinate, end product of the -ketoadipate pathway. Indeed, the in vitro -ketoadipate-succinyl coenzyme A transferase activity was seen to be inhibited by succinate, a coproduct of the reaction.
Microorganisms, 2015
Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great int... more Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h(-1) at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h(-1) and D. geothermalis DSM-11302 biomass reached 1.4 g·L(-1) in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc(-1); cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX(-1)·h(-1), respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture.
Biotechnology, Agronomy, Society and Environment
Heterogeneities caused by deficient mixing in large-scale bioreactors have been identified and de... more Heterogeneities caused by deficient mixing in large-scale bioreactors have been identified and described in literature. These heterogeneities affect physiological changes of microorganisms through its passage in different zones of concentrations. Consequently the differences in terms of productivities, qualities and/or yields of products of interest have been observed during scaling-up from laboratory to larger scales. For this reason, large-scale process improvement depends on the understanding of dynamic interactions between microbial responses and physical phenomena inside bioreactors. The dynamic responses of microorganisms are used as a tool for gaining insight into the fundamentals of microbial changes under a mixing-well controlled environment. Our research group has not only applied scale-down methodology to study the microbial responses at molecular, microscopic and macroscopic levels of observation, but also has used innovative strains and process engineering tools to eval...
Enrichment of the medium with yeast extract (20 g.l ) and Tryptone (40 g.l ) increased the growth... more Enrichment of the medium with yeast extract (20 g.l ) and Tryptone (40 g.l ) increased the growth of Lactobacillus casei ssp. rhamnosusand its production of lactic acid in both batch and cell-recycle cultures without affecting glucose consumption and the lactic acid production rate.
Process Biochemistry, 2014
Carbon dioxide (CO 2 ) is a major compound of microbial metabolism both as a substrate and as a p... more Carbon dioxide (CO 2 ) is a major compound of microbial metabolism both as a substrate and as a product but high dissolved carbon dioxide concentrations have long been known to affect yeast physiology.
Extremophiles, 2014
Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have be... more Few studies concerning the nutritional requirements of Deinococcus geothermalis DSM 11300 have been conducted to date. Three defined media compositions have been published for the growth of this strain but they were found to be inadequate to achieve growth without limitation. Furthermore, growth curves, biomass concentration and growth rates were generally not available. Analysis in Principal Components was used in this work to compare and consequently to highlight the main compounds which differ between published chemically defined media. When available, biomass concentration, and/or growth rate were superimposed to the PCA analysis. The formulations of the media were collected from existing literature; media compositions designed for the growth of several strains of Deinococcaceae or Micrococcaceae were included. The results showed that a defined medium adapted from Holland et al. (Appl Microbiol Biotechnol 72:1074-1082, 2006) was the best basal medium and was chosen for further studies. A growth rate of 0.03 h(-1) and a final OD600nm of 0.55 were obtained, but the growth was linear. Then, the effects of several medium components on oxygen uptake and biomass production by Deinococcus geothermalis DSM 11300 were studied using a respirometry-based method, to search for the nutritional limitation. The results revealed that the whole yeast extract in the medium with glucose is necessary to obtain a non-limiting growth of Deinococcus geothermalis DSM 11300 at a maximum growth rate of 0.64 h(-1) at 45 °C.
Mathematics and Computers in Simulation, 2004
We present modelling software developed under MATLAB in which parameter estimations are obtained ... more We present modelling software developed under MATLAB in which parameter estimations are obtained by using non-linear regression techniques. The different parameters appear in a set of non-linear algebraic and differential equations representing the model of the process. From experimental data obtained in discontinuous cultures a representative mathematical model (unstructured kinetic model) of the macroscopic behaviour of Lactobacillus acidophilus has been developed. An unstructured model expressed the specific rates of cell growth, lactic acid production and glucose consumption for batch fermentation. The model is formulated by considering the inhibition of growth under sub-optimal culture conditions during Lactobacillus acidophilus fermentation, which is accompanied by an increase of the maintenance energy. This study permits to predict the cellular behaviour at low growth temperatures and enables to define the response of the strain to sub-optimal temperature stress.
Journal of Chromatography A, 2011
Response surface methodology (RSM) was used for the determination of optimum extraction parameter... more Response surface methodology (RSM) was used for the determination of optimum extraction parameters to reach maximum lipid extraction yield with yeast. Total lipids were extracted from oleaginous yeast (Rhodotorula glutinis) using pressurized liquid extraction (PLE). The effects of extraction parameters on lipid extraction yield were studied by employing a second-order central composite design. The optimal condition was obtained as three cycles of 15 min at 100 • C with a ratio of 144 g of hydromatrix per 100 g of dry cell weight. Different analysis methods were used to compare the optimized PLE method with two conventional methods (Soxhlet and modification of Bligh and Dyer methods) under efficiency, selectivity and reproducibility criteria thanks to gravimetric analysis, GC with flame ionization detector, High Performance Liquid Chromatography linked to Evaporative Light Scattering Detector (HPLC-ELSD) and thin-layer chromatographic analysis. For each sample, the lipid extraction yield with optimized PLE was higher than those obtained with referenced methods (Soxhlet and Bligh and Dyer methods with, respectively, a recovery of 78% and 85% compared to PLE method). Moreover, the use of PLE led to major advantages such as an analysis time reduction by a factor of 10 and solvent quantity reduction by 70%, compared with traditional extraction methods.
International Journal of Modelling, Identification and Control, 2008
... Carine Bideaux,* Gérard Goma and Jean-Louis Uribelarrea Université de Toulouse, INSA, UPS, IN... more ... Carine Bideaux,* Gérard Goma and Jean-Louis Uribelarrea Université de Toulouse, INSA, UPS, INP; LISBP, I135 Avenue de Rangueil, Toulouse F-31077, France ... Jean-Louis Uribelarrea received his PhD in Microbial Engineering from INSA Toulouse, France, in July 1980. ...
Enzyme and Microbial Technology, 2002
Three inducible and extracellular activities produced by Bacillus subtilis NCIMB 11871 and 11872 ... more Three inducible and extracellular activities produced by Bacillus subtilis NCIMB 11871 and 11872 were identified: a fructosyl transferase, a sucrase and a polymerase activity synthesising fructose polymers. These polymers are responsible for a limitation in the oxygen transfer, probably by increasing the viscosity of the culture medium, and for an opalescent supernatant observed at the end of the exponential growth phase. The production and degradation of the three enzymatic activities was tightly coupled during the time course of micro-organism cultivation. Furthermore, no separation of them was achieved by ammonium sulphate precipitation, ultrafiltration and other separation techniques. We suggest that these three activities are supported by the same enzyme, and that this enzyme is a levansucrase.