In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

P Maia, M Rocha, I Rocha - Microbiology and Molecular Biology …, 2016 - Am Soc Microbiol
Shifting from chemical to biotechnological processes is one of the cornerstones of 21st
century industry. The production of a great range of chemicals via biotechnological means is …

Algal cell factories: approaches, applications, and potentials

W Fu, A Chaiboonchoe, B Khraiwesh, DR Nelson… - Marine Drugs, 2016 - mdpi.com
With the advent of modern biotechnology, microorganisms from diverse lineages have been
used to produce bio-based feedstocks and bioactive compounds. Many of these compounds …

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum

V Villanova, AE Fortunato, D Singh… - … of the Royal …, 2017 - royalsocietypublishing.org
Diatoms are prominent marine microalgae, interesting not only from an ecological point of
view, but also for their possible use in biotechnology applications. They can be cultivated in …

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

A von Kamp, S Klamt - Nature communications, 2017 - nature.com
Computational modelling of metabolic networks has become an established procedure in
the metabolic engineering of production strains. One key principle that is frequently used to …

Genome-scale model reveals metabolic basis of biomass partitioning in a model diatom

J Levering, J Broddrick, CL Dupont, G Peers, K Beeri… - PloS one, 2016 - journals.plos.org
Diatoms are eukaryotic microalgae that contain genes from various sources, including
bacteria and the secondary endosymbiotic host. Due to this unique combination of genes …

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

S Klamt, G Regensburger, MP Gerstl… - PLoS computational …, 2017 - journals.plos.org
Elementary flux modes (EFMs) emerged as a formal concept to describe metabolic
pathways and have become an established tool for constraint-based modeling and …

On the feasibility of growth-coupled product synthesis in microbial strains

S Klamt, R Mahadevan - Metabolic engineering, 2015 - Elsevier
Enforcing obligate coupling of growth with synthesis of a desired product has become a key
principle for metabolic engineering of microbial production strains. Various methods from …

Reconstruction of the microalga Nannochloropsis salina genome-scale metabolic model with applications to lipid production

N Loira, S Mendoza, M Paz Cortés, N Rojas… - BMC systems …, 2017 - Springer
Abstract Background Nannochloropsis salina (= Eustigmatophyceae) is a marine microalga
which has become a biotechnological target because of its high capacity to produce …

Metabolomics integrated elementary flux mode analysis in large metabolic networks

MP Gerstl, DE Ruckerbauer, D Mattanovich… - Scientific reports, 2015 - nature.com
Elementary flux modes (EFMs) are non-decomposable steady-state pathways in metabolic
networks. They characterize phenotypes, quantify robustness or identify engineering targets …

Metabolic modelling links Warburg effect to collagen formation, angiogenesis and inflammation in the tumoral stroma

M Mahout, L Schwartz, R Attal, A Bakkar, S Peres - PloS one, 2024 - journals.plos.org
Cancer cells are known to express the Warburg effect—increased glycolysis and formation
of lactic acid even in the presence of oxygen—as well as high glutamine uptake. In tumors …