LIVIVO - Search results -

Search results

Result 1 - 10 of total 86

Search options

Article ; Online: Qualitative Modeling, Analysis and Control of Synthetic Regulatory Circuits.

Chaves, Madalena / de Jong, Hidde

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2229, Page(s) 1–40

Abstract: Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide ... ...

Abstract	Qualitative modeling approaches are promising and still underexploited tools for the analysis and design of synthetic circuits. They can make predictions of circuit behavior in the absence of precise, quantitative information. Moreover, they provide direct insight into the relation between the feedback structure and the dynamical properties of a network. We review qualitative modeling approaches by focusing on two specific formalisms, Boolean networks and piecewise-linear differential equations, and illustrate their application by means of three well-known synthetic circuits. We describe various methods for the analysis of state transition graphs, discrete representations of the network dynamics that are generated in both modeling frameworks. We also briefly present the problem of controlling synthetic circuits, an emerging topic that could profit from the capacity of qualitative modeling approaches to rapidly scan a space of design alternatives.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Computer Simulation ; Gene Regulatory Networks ; Models, Genetic
Language	English
Publishing date	2021-01-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1032-9_1
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains.

Baldazzi, Valentina / Ropers, Delphine / Gouzé, Jean-Luc / Gedeon, Tomas / de Jong, Hidde

eLife

2023 Volume 12

Abstract: Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to ... ...

Abstract	Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of
MeSH term(s)	Escherichia coli/metabolism ; Proteomics ; Metabolic Engineering/methods ; Ribosomes ; Resource Allocation
Language	English
Publishing date	2023-05-31
Publishing country	England
Document type	Journal Article
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.79815
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Optimal protein production by a synthetic microbial consortium: coexistence, distribution of labor, and syntrophy.

Martínez, Carlos / Cinquemani, Eugenio / Jong, Hidde de / Gouzé, Jean-Luc

Journal of mathematical biology

2023 Volume 87, Issue 1, Page(s) 23

Abstract: The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon ...

Abstract	The bacterium E. coli is widely used to produce recombinant proteins such as growth hormone and insulin. One inconvenience with E. coli cultures is the secretion of acetate through overflow metabolism. Acetate inhibits cell growth and represents a carbon diversion, which results in several negative effects on protein production. One way to overcome this problem is the use of a synthetic consortium of two different E. coli strains, one producing recombinant proteins and one reducing the acetate concentration. In this paper, we study a mathematical model of such a synthetic community in a chemostat where both strains are allowed to produce recombinant proteins. We give necessary and sufficient conditions for the existence of a coexistence equilibrium and show that it is unique. Based on this equilibrium, we define a multi-objective optimization problem for the maximization of two important bioprocess performance metrics, process yield and productivity. Solving numerically this problem, we find the best available trade-offs between the metrics. Under optimal operation of the mixed community, both strains must produce the protein of interest, and not only one (distribution instead of division of labor). Moreover, in this regime acetate secretion by one strain is necessary for the survival of the other (syntrophy). The results thus illustrate how complex multi-level dynamics shape the optimal production of recombinant proteins by synthetic microbial consortia.
MeSH term(s)	Microbial Consortia ; Escherichia coli/metabolism ; Recombinant Proteins/metabolism ; Acetates/metabolism ; Insulin/metabolism
Chemical Substances	Recombinant Proteins ; Acetates ; Insulin
Language	English
Publishing date	2023-07-03
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187101-8
ISSN	1432-1416 ; 0303-6812
ISSN (online)	1432-1416
ISSN	0303-6812
DOI	10.1007/s00285-023-01935-3
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1495: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Maturation models of fluorescent proteins are necessary for unbiased estimates of promoter activity.

Pavlou, Antrea / Cinquemani, Eugenio / Geiselmann, Johannes / de Jong, Hidde

Biophysical journal

2022 Volume 121, Issue 21, Page(s) 4179–4188

Abstract: Fluorescent proteins (FPs) are a powerful tool to quantitatively monitor gene expression. The dynamics of a promoter and its regulation can be inferred from fluorescence data. The interpretation of fluorescent data, however, is strongly dependent on the ... ...

Abstract	Fluorescent proteins (FPs) are a powerful tool to quantitatively monitor gene expression. The dynamics of a promoter and its regulation can be inferred from fluorescence data. The interpretation of fluorescent data, however, is strongly dependent on the maturation of FPs since different proteins mature in distinct ways. We propose a novel approach for analyzing fluorescent reporter data by incorporating maturation dynamics in the reconstruction of promoter activities. Our approach consists of developing and calibrating mechanistic maturation models for distinct FPs. These models are then used alongside a Bayesian approach to estimate promoter activities from fluorescence data. We demonstrate by means of targeted experiments in Escherichia coli that our approach provides robust estimates and that accounting for maturation is, in many cases, essential for the interpretation of gene expression data.
MeSH term(s)	Bayes Theorem ; Luminescent Proteins/genetics ; Luminescent Proteins/metabolism ; Promoter Regions, Genetic ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Green Fluorescent Proteins/genetics ; Green Fluorescent Proteins/metabolism
Chemical Substances	Luminescent Proteins ; Green Fluorescent Proteins (147336-22-9)
Language	English
Publishing date	2022-09-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2022.09.021
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 2: Show issues

Order via subito

Details ▾

Article ; Online: Resource allocation accounts for the large variability of rate-yield phenotypes across bacterial strains

Valentina Baldazzi / Delphine Ropers / Jean-Luc Gouzé / Tomas Gedeon / Hidde de Jong

eLife, Vol

2023 Volume 12

Abstract	Different strains of a microorganism growing in the same environment display a wide variety of growth rates and growth yields. We developed a coarse-grained model to test the hypothesis that different resource allocation strategies, corresponding to different compositions of the proteome, can account for the observed rate-yield variability. The model predictions were verified by means of a database of hundreds of published rate-yield and uptake-secretion phenotypes of Escherichia coli strains grown in standard laboratory conditions. We found a very good quantitative agreement between the range of predicted and observed growth rates, growth yields, and glucose uptake and acetate secretion rates. These results support the hypothesis that resource allocation is a major explanatory factor of the observed variability of growth rates and growth yields across different bacterial strains. An interesting prediction of our model, supported by the experimental data, is that high growth rates are not necessarily accompanied by low growth yields. The resource allocation strategies enabling high-rate, high-yield growth of E. coli lead to a higher saturation of enzymes and ribosomes, and thus to a more efficient utilization of proteomic resources. Our model thus contributes to a fundamental understanding of the quantitative relationship between rate and yield in E. coli and other microorganisms. It may also be useful for the rapid screening of strains in metabolic engineering and synthetic biology.
Keywords	resource allocation ; growth rate ; growth yield ; bacterial physiology ; metabolic regulation ; Escherichia coli ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2023-05-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Optimal proteome allocation and the temperature dependence of microbial growth laws

Francis Mairet / Jean-Luc Gouzé / Hidde de Jong

npj Systems Biology and Applications, Vol 7, Iss 1, Pp 1-

2021 Volume 11

Abstract: Abstract Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial ...

Abstract	Abstract Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.
Keywords	Biology (General) ; QH301-705.5
Subject code	669
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Optimal proteome allocation and the temperature dependence of microbial growth laws.

Mairet, Francis / Gouzé, Jean-Luc / de Jong, Hidde

NPJ systems biology and applications

2021 Volume 7, Issue 1, Page(s) 14

Abstract: Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, ... ...

Abstract	Although the effect of temperature on microbial growth has been widely studied, the role of proteome allocation in bringing about temperature-induced changes remains elusive. To tackle this problem, we propose a coarse-grained model of microbial growth, including the processes of temperature-sensitive protein unfolding and chaperone-assisted (re)folding. We determine the proteome sector allocation that maximizes balanced growth rate as a function of nutrient limitation and temperature. Calibrated with quantitative proteomic data for Escherichia coli, the model allows us to clarify general principles of temperature-dependent proteome allocation and formulate generalized growth laws. The same activation energy for metabolic enzymes and ribosomes leads to an Arrhenius increase in growth rate at constant proteome composition over a large range of temperatures, whereas at extreme temperatures resources are diverted away from growth to chaperone-mediated stress responses. Our approach points at risks and possible remedies for the use of ribosome content to characterize complex ecosystems with temperature variation.
MeSH term(s)	Bacteria/growth & development ; Computer Simulation ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Gene Expression/genetics ; Gene Expression Regulation, Bacterial/genetics ; Models, Biological ; Models, Theoretical ; Nutrients/metabolism ; Proteome/metabolism ; Proteome/physiology ; Proteomics/methods ; Ribosomes ; Systems Biology/methods ; Temperature
Chemical Substances	Escherichia coli Proteins ; Proteome
Language	English
Publishing date	2021-03-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2056-7189
ISSN (online)	2056-7189
DOI	10.1038/s41540-021-00172-y
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate.

Pinhal, Stéphane / Ropers, Delphine / Geiselmann, Johannes / de Jong, Hidde

Journal of bacteriology

2019 Volume 201, Issue 13

Abstract: During aerobic growth on glucose, ...

Abstract	During aerobic growth on glucose,
MeSH term(s)	Acetates/metabolism ; Biological Transport ; Escherichia coli/genetics ; Escherichia coli/growth & development ; Fermentation ; Gene Expression Regulation, Bacterial ; Glucose/metabolism ; Metabolic Networks and Pathways ; Mutation
Chemical Substances	Acetates ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2019-06-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2968-3
ISSN	1098-5530 ; 0021-9193
ISSN (online)	1098-5530
ISSN	0021-9193
DOI	10.1128/JB.00147-19
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Ud II Zs.50: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs.

Mauri, Marco / Gouzé, Jean-Luc / de Jong, Hidde / Cinquemani, Eugenio

PLoS computational biology

2020 Volume 16, Issue 4, Page(s) e1007795

Abstract: Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, ... ...

Abstract	Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species.
MeSH term(s)	Escherichia coli/genetics ; Escherichia coli/metabolism ; Metabolic Engineering/methods ; Microbiota/genetics ; Microbiota/physiology ; Models, Biological ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; Synthetic Biology/methods
Chemical Substances	Recombinant Proteins
Language	English
Publishing date	2020-04-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2193340-6
ISSN	1553-7358 ; 1553-734X
ISSN (online)	1553-7358
ISSN	1553-734X
DOI	10.1371/journal.pcbi.1007795
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Enhanced production of heterologous proteins by a synthetic microbial community

Marco Mauri / Jean-Luc Gouzé / Hidde de Jong / Eugenio Cinquemani

PLoS Computational Biology, Vol 16, Iss 4, p e

Conditions and trade-offs.

2020 Volume 1007795

Abstract	Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

Full text online

Full text

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

To top

Your last searches

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Inter-library loan at ZB MED