scholarly journals Model-based Identification of Some Conditions Leading to Glycolytic Oscillations in E. coli Cells

2019 ◽  
Vol 32 (4) ◽  
pp. 523-533 ◽  
Author(s):  
G. Maria
Keyword(s):  
E Coli ◽  
Glycolytic Oscillations ◽  
Model Based

scholarly journals Inclusion Body Bead Size in E. coli Controlled by Physiological Feeding

2018 ◽  
Vol 6 (4) ◽  
pp. 116 ◽  
Author(s):  
Julian Kopp ◽  
Christoph Slouka ◽  
Daniel Strohmer ◽  
Julian Kager ◽  
Oliver Spadiut ◽  
...  
Keyword(s):  
Body Size ◽  
Inclusion Body ◽  
Uptake Rate ◽  
Inclusion Bodies ◽  
Downstream Processing ◽  
Sugar Uptake ◽  
E Coli ◽  
Model Based ◽  
Bead Size

The Gram-negative bacterium E. coli is the host of choice for producing a multitude of recombinant proteins relevant in the pharmaceutical industry. Generally, cultivation is easy, media are cheap, and a high product titer can be obtained. However, harsh induction procedures combined with the usage of IPTG (isopropyl β-d-1 thiogalactopyranoside) as an inducer are often believed to cause stress reactions, leading to intracellular protein aggregates, which are so known as so-called inclusion bodies (IBs). Downstream applications in bacterial processes cause the bottleneck in overall process performance, as bacteria lack many post-translational modifications, resulting in time and cost-intensive approaches. Especially purification of inclusion bodies is notoriously known for its long processing times and low yields. In this contribution, we present screening strategies for determination of inclusion body bead size in an E. coli-based bioprocess producing exclusively inclusion bodies. Size can be seen as a critical quality attribute (CQA), as changes in inclusion body behavior have a major effect on subsequent downstream processing. A model-based approach was used, aiming to trigger a distinct inclusion body size: Physiological feeding control, using qs,C as a critical process parameter, has a high impact on inclusion body size and could be modelled using a hyperbolic saturation mechanism calculated in form of a cumulated substrate uptake rate. Within this model, the sugar uptake rate of the cells, in the form of the cumulated sugar uptake-value, was simulated and considered being a key performance indicator for determination of the desired size. We want to highlight that the usage of the mentioned screening strategy in combination with a model-based approach will allow tuning of the process towards a certain inclusion body size using a qs based control only. Optimized inclusion body size at the time-point of harvest should stabilize downstream processing and, therefore, increase the overall time-space yield. Furthermore, production of distinct inclusion body size may be interesting for application as a biocatalyst and nanoparticulate material.

Model-Based Optimization of the Cultivation Process for Recombinant Virus Capsid Proteins in E. coli

2001 ◽  
Vol 34 (5) ◽  
pp. 299-303 ◽  
Author(s):  
E. Franco-Lara ◽  
V. Galvanauskas ◽  
N. Volk ◽  
A. Lübbert
Keyword(s):  
Recombinant Virus ◽  
Capsid Proteins ◽  
Virus Capsid ◽  
E Coli ◽  
Model Based ◽  
Cultivation Process

scholarly journals Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering

2007 ◽  
Vol 7 (1) ◽  
pp. 34 ◽  
Author(s):  
Marjan De Mey ◽  
Jo Maertens ◽  
Gaspard J Lequeux ◽  
Wim K Soetaert ◽  
Erick J Vandamme
Keyword(s):  
Metabolic Engineering ◽  
E Coli ◽  
Model Based ◽  
Promoter Library ◽  
Indispensable Tool ◽  
Model Based Analysis

New beach in a shallow estuarine lagoon: a model-based E. coli pollution risk assessment

2018 ◽  
Vol 22 (3) ◽  
pp. 573-586 ◽  
Author(s):  
Georg Umgiesser ◽  
Natalja Čerkasova ◽  
Ali Erturk ◽  
Jovita Mėžinė ◽  
Marija Kataržytė
Keyword(s):  
Risk Assessment ◽  
Pollution Risk ◽  
E Coli ◽  
Model Based ◽  
Estuarine Lagoon

scholarly journals Modeling predicts that CRISPR-based activators, unlike CRISPR-based repressors, scale well with increasing gRNA competition and dCas9 bottlenecking

2019 ◽  
Author(s):  
Samuel Clamons ◽  
Richard Murray
Keyword(s):  
Simple Model ◽  
Transcriptional Networks ◽  
E Coli ◽  
Model Based ◽  
Fold Activation

AbstractSynthetic transcriptional networks built from CRISPR-based repressors (CRISPRi) rely on shared use of a core dCas9 protein. In E. coli, CRISPRi cannot support more than about a dozen simultaneous gRNAs before the fold repression of any individual gRNA drops below 10x. We show with a simple model based on previous characterization of competition in CRISPRi that activation by CRISPR-based activators (CRISPRa) is much less sensitive to dCas9 bottle-necking than CRISPRi. We predict that E. coli should be able to support dozens to hundreds of CRISPRa gRNAs at >10-fold activation.

Representation, abstraction, and simple-minded sophisticates

2020 ◽  
Vol 43 ◽  
Author(s):  
Peter Dayan
Keyword(s):  
Decision Theory ◽  
Predictive Coding ◽  
Bayesian Decision Theory ◽  
Bayesian Decision ◽  
Model Based ◽  
Model Free

Abstract Bayesian decision theory provides a simple formal elucidation of some of the ways that representation and representational abstraction are involved with, and exploit, both prediction and its rather distant cousin, predictive coding. Both model-free and model-based methods are involved.

Endotoxin Alteration of the Mucopolysaccharide Blood Vessel Coating in Rats

1974 ◽  
Vol 32 ◽  
pp. 148-149
Author(s):  
D. E. Philpott ◽  
A. Takahashi
Keyword(s):  
Skeletal Muscle ◽  
Endothelial Cells ◽  
Salivary Gland ◽  
Carotid Artery ◽  
Basement Membrane ◽  
Coronary Vessels ◽  
Ruthenium Red ◽  
E Coli ◽  
Old Rats ◽  
The Brain

Two month, eight month and two year old rats were treated with 10 or 20 mg/kg of E. Coli endotoxin I. P. The eight month old rats proved most resistant to the endotoxin. During fixation the aorta, carotid artery, basil arartery of the brain, coronary vessels of the heart, inner surfaces of the heart chambers, heart and skeletal muscle, lung, liver, kidney, spleen, brain, retina, trachae, intestine, salivary gland, adrenal gland and gingiva were treated with ruthenium red or alcian blue to preserve the mucopolysaccharide (MPS) coating. Five, 8 and 24 hrs of endotoxin treatment produced increasingly marked capillary damage, disappearance of the MPS coating, edema, destruction of endothelial cells and damage to the basement membrane in the liver, kidney and lung.

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