Multi-objective optimization of genome-scale metabolic models: the case of ethanol production

Ethanol is among the largest fermentation product used worldwide, accounting for more than 90% of all biofuel produced in the last decade. However current production methods of ethanol are unable to meet the requirements of increasing global demand, because of low yields on glucose sources. In this work, we present an in silico multi-objective optimization and analyses of eight genome-scale metabolic networks for the overproduction of ethanol within the engineered cell. We introduce MOME (multi-objective metabolic engineering) algorithm, that models both gene knockouts and enzymes up and down regulation using the Redirector framework. In a multi-step approach, MOME tackles the multi-objective optimization of biomass and ethanol production in the engineered strain; and performs genetic design and clustering analyses on the optimization results. We find in silico E. coli Pareto optimal strains with a knockout cost of 14 characterized by an ethanol production up to 19.74mmolgDW−1h−1 (+832.88% with respect to wild-type) and biomass production of 0.02h−1 (−98.06% ). The analyses on E. coli highlighted a single knockout strategy producing 16.49mmolgDW−1h−1 (+679.29% ) ethanol, with biomass equals to 0.23h−1 (−77.45% ). We also discuss results obtained by applying MOME to metabolic models of: (i) S. aureus; (ii) S. enterica; (iii) Y. pestis; (iv) S. cerevisiae; (v) C. reinhardtii; (vi) Y. lipolytica. We finally present a set of simulations in which constrains over essential genes and minimum allowable biomass were included. A bound over the maximum allowable biomass was also added, along with other settings representing rich media compositions. In the same conditions the maximum improvement in ethanol production is +195.24%

Dynamic metabolic control: towards precision engineering of metabolism

Advances in metabolic engineering have led to the synthesis of a wide variety of valuable chemicals in microorganisms. The key to commercializing these processes is the improvement of titer, productivity, yield, and robustness. Traditional approaches to enhancing production use the “push–pull-block” strategy that modulates enzyme expression under static control. However, strains are often optimized for specific laboratory set-up and are sensitive to environmental fluctuations. Exposure to sub-optimal growth conditions during large-scale fermentation often reduces their production capacity. Moreover, static control of engineered pathways may imbalance cofactors or cause the accumulation of toxic intermediates, which imposes burden on the host and results in decreased production. To overcome these problems, the last decade has witnessed the emergence of a new technology that uses synthetic regulation to control heterologous pathways dynamically, in ways akin to regulatory networks found in nature. Here, we review natural metabolic control strategies and recent developments in how they inspire the engineering of dynamically regulated pathways. We further discuss the challenges of designing and engineering dynamic control and highlight how model-based design can provide a powerful formalism to engineer dynamic control circuits, which together with the tools of synthetic biology, can work to enhance microbial production

Advancing microbial sciences by individual-based modelling

Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE)

PROSTAGLANDIN E2: ANALYSIS OF EFFECTS ON PREGNANCY AND CORPUS LUTEUM IN HAMSTERS AND RATS

ABSTRACT Effects of prostaglandin (PG) E2 on some reproductive processes of hamsters and rats were studied. The PG exerted antifertility effects in either species although it was 4–10 times less potent than PGF2α. Antifertility doses of PGE2 caused morphological degeneration of corpora lutea, induced fresh ovulations during the course of the treatment, significantly decreased peripheral progesterone levels and inhibited development of deciduomata in response to trauma. Both pregnancy and decidual growth could be maintained by simultaneous administration of exogenous progesterone. PGE2 also decreased plasma progesterone concentration in pseudopregnant-hysterectomized hamsters although the decrease was not significant when compared with intact pregnant or pseudopregnant hamsters. PGE2 produced no demonstrable effects on egg transport in hamsters but may have induced delayed implantation in rats by causing tubal retention of zygotes. The antifertility doses of PGE2 but not of PGF2α inhibited implantation of a proportion of blastocysts as studied by the Pontamine blue reaction and adversely affected the spacing mechanism of blastocysts in the uterus significantly reducing the distance between the adjacent implantation sites. When PGs E2 and F2α were given together to pregnant rats in doses which were virtually ineffective individually, the combined treatment caused loss of pregnancy. Administration of PGE2 to near term hamsters produced premature littering but oxytocin in doses tried proved inactive. Antifertility doses of PGE2 produced diarrhoea in rats but not in hamsters. The results demonstrate that PGE2 shares the luteolytic property of PGF2α but in addition possesses several other properties not known to be shared by PGF2α.</jats:p