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%

A comparative study of egg mass and clutch size in the Anseriformes

The factors explaining interspecific differences in clutch investment in precocial birds are poorly understood. We investigated how variations in clutch characteristics are related to environmental factors in a comparative study of 151 extant species of ducks, geese and swans (Anseriformes). Egg mass was negatively related to clutch size in a phylogenetic regression, a relationship that was much stronger when controlling for female mass. Nest placement was related to both egg size and clutch size, with cavity-nesting species laying more but smaller eggs. Egg size was positively correlated with incubation period and with female mass, and also with sexual size dimorphism (i.e. male mass relative to that of the female). Clutch size was not related to female mass. Species with long term pair bonds laid smaller clutches and larger eggs. The size of the breeding range was strongly positively correlated with clutch size and clutch mass, and its inclusion in multivariate models made other biogeographical variables (hemisphere, breeding latitude or insularity) non-significant. The small clutches in insular species appear to be a product of small range size rather than insularity per se. Our results suggest there is an evolutionary trade-off between clutch and egg size, and lend support to Lack’s resource-limitation hypothesis for the waterfowl.Peer reviewe