Related Experiment Video
Updated: Jun 4, 2026
08:01
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Mechanistic pathway modeling for industrial biotechnology: challenging but worthwhile
Wolfgang Wiechert1, Stephan Noack
1Institute of Bio and Geo Sciences, IBG-1: Biotechnology Forschungszentrum Jülich, Wilhelm-Johnen-Str., D-52428 Jülich, Germany. w.wiechert@fz-juelich.de
Current Opinion in Biotechnology
|March 1, 2011
Summary
Mechanistic models quantitatively describe biochemical pathways using network structure and kinetics. Recent advances in systems biology enable large-scale metabolic network modeling for industrial biotechnology bioprocess development.
Area of Science:
- Biochemistry
- Systems Biology
- Industrial Biotechnology
Background:
- Mechanistic (kinetic) models quantitatively describe biochemical pathways.
- These models integrate network structure, regulatory information, and reaction kinetics.
- The field has evolved significantly with the data-rich era of systems biology.
Purpose of the Study:
- Focus on recent developments and challenges in metabolic network modeling.
- Highlight applications in industrial biotechnology and bioprocess development.
Main Methods:
- Quantitative description of dynamic and steady states of biochemical pathways.
- Integration of stoichiometry, regulatory information, and reaction kinetics.
- Development and validation of large-scale, genome-scale mechanistic models.
Main Results:
- Availability of extensive data for validating and testing models.
- Increased capacity for building large mechanistic models.
- Shift towards data-rich approaches in systems biology.
Conclusions:
- Mechanistic modeling is crucial for understanding and predicting biochemical network behavior.
- Metabolic network modeling is central to advancements in industrial biotechnology.
- The field is rapidly advancing due to systems biology and data availability.
Related Concept Videos
01:22Bioreactor Controls-III
Strain improvement is a foundational strategy in industrial microbiology aimed at maximizing microbial productivity, particularly because natural isolates typically yield commercially valuable products in very low concentrations. Although optimizing the culture medium and environmental conditions can improve yields, these adjustments are inherently limited by the organism’s genetic potential. As a result, the focus shifts toward genetic modifications to enhance biosynthetic capacity. The...
01:27Upstream Processing
Upstream processing represents a critical phase in biomanufacturing, wherein biological systems such as microorganisms, mammalian cells, or insect cells are cultivated to produce therapeutic proteins, vaccines, enzymes, or other biologically derived products. This phase encompasses all steps from the selection and genetic manipulation of the production organism to the cultivation of cells in bioreactors under tightly controlled environmental conditions.Host Selection and Genetic OptimizationThe...
01:14Scale-Up Processes
The scale-up of microbial fermentation processes is essential in industrial biotechnology, allowing the transition from laboratory-scale experiments to commercial-scale production while aiming to maintain product yield and quality. This process requires meticulous adjustment of equipment design, process parameters, and contamination control strategies to accommodate increasing culture volumes.At the laboratory scale, cultures are typically maintained in 1 to 10-liter glass or autoclavable...
01:30Production of Pharmaceuticals
Industrial insulin production uses genetically engineered E. coli expressing a proinsulin gene controlled by a tryptophan promoter and containing a methionine linker for later cleavage. The cells also carry ampicillin resistance for selective growth. Seed cultures are stored at −80 °C and production begins by thawing a small amount to inoculate starter cultures, which are progressively scaled to a 50,000-L bioreactor. In the bioreactor, E. coli grow in nutrient-rich media under sterile, tightly...
01:28Microbial Bioremediation of Plastics
Polyethylene terephthalate (PET) is a synthetic polymer widely utilized in the packaging industry, particularly for bottles and containers. Due to its chemical stability and durability, PET accumulates in the environment, contributing significantly to plastic pollution. It comprises repeating units of terephthalic acid and ethylene glycol, resulting in a semi-crystalline structure that is resistant to natural degradation processes.A notable breakthrough in plastic biodegradation came with the...
01:24Other Glycolytic Pathways
The pentose phosphate pathway (PPP) operates in parallel with glycolysis, facilitating the metabolism of both pentoses and glucose. This pathway consists of two distinct phases: the oxidative and non-oxidative phases. While it does not directly generate ATP, the intermediates formed during the process can integrate into glycolysis, contributing to cellular energy metabolism when required.Oxidative Phase: NADPH ProductionThe oxidative phase of the pentose phosphate pathway is primarily...