Multiscale metabolic modeling of C4 plants: connecting nonlinear genome-scale models to leaf-scale metabolism in developing maize leaves

C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, here the predicted fluxes achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems. We suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data.Comment: 57 pages, 14 figures; submitted to PLoS Computational Biology; source code available at http://github.com/ebogart/fluxtools and http://github.com/ebogart/multiscale_c4_sourc

Biomass from microalgae: The potential of domestication towards sustainable biofactories

Interest in bulk biomass from microalgae, for the extraction of high-value nutraceuticals, bio-products, animal feed and as a source of renewable fuels, is high. Advantages of microalgal vs. plant biomass production include higher yield, use of non-arable land, recovery of nutrients from wastewater, efficient carbon capture and faster development of new domesticated strains. Moreover, adaptation to a wide range of environmental conditions evolved a great genetic diversity within this polyphyletic group, making microalgae a rich source of interesting and useful metabolites. Microalgae have the potential to satisfy many global demands; however, realization of this potential requires a decrease of the current production costs. Average productivity of the most common industrial strains is far lower than maximal theoretical estimations, suggesting that identification of factors limiting biomass yield and removing bottlenecks are pivotal in domestication strategies aimed to make algal-derived bio-products profitable on the industrial scale. In particular, the light-to-biomass conversion efficiency represents a major constraint to finally fill the gap between theoretical and industrial productivity. In this respect, recent results suggest that significant yield enhancement is feasible. Full realization of this potential requires further advances in cultivation techniques, together with genetic manipulation of both algal physiology and metabolic networks, to maximize the efficiency with which solar energy is converted into biomass and bio-products. In this review, we draft the molecular events of photosynthesis which regulate the conversion of light into biomass, and discuss how these can be targeted to enhance productivity through mutagenesis, strain selection or genetic engineering. We outline major successes reached, and promising strategies to achieving significant contributions to future microalgae-based biotechnology

Aerospace medicine and biology: A continuing bibliography with indexes, supplement 204

This bibliography lists 140 reports, articles, and other documents introduced into the NASA scientific and technical information system in February 1980

Improving distribution and absorption of light in microalgal photobioreactors through plasmon enhancement, entrapped cultivation and controlled motion

Microalgae represent a promising source of renewable biomass for the production of biofuels and valuable chemicals. However, the development of high throughput microalgal cultivation methods and energy efficient biomass harvesting technology is necessary to improve the economic viability of large scale microalgal biomass production. The issue of poor distribution and absorption of light is one of the hurdle that can be addressed to improve the productivity in microalgal cultivation systems. As it happens, microalgal photosynthetic activities have shown great dependence on the irradiance to which the microalgal cells are exposed. Quantitatively, microalgal growth increases with increasing light intensity until a saturation level beyond which the microalgal photosynthetic machinery can be subject to photodamage. Qualitatively, most microalgal species have exhibited a propensity for wavelengths in the blue and red regions of the visible electromagnetic spectrum whereas other wavelengths can induce photoinhibition. Further, a change in the incident light can lead to photoacclimation where the microalgal species activate the preferential synthesis of certain compounds or completely alter their metabolic activity. Despite such importance of light for microalgal growth and biomass production, only a small fraction of microalgal cells receives an optimal irradiance in current microalgal cultivation systems (open and enclosed ponds). The remaining microalgal cells are found either in the over illuminated zones (e.g. top surface of open culture) of the cultivation systems where they are exposed to photoinhibition or in the poorly illuminated zones where their growth is limited. In this dissertation, this issue is addressed by developing a multi-fold approach to improve the distribution and absorption of light in microalgal photobioreactors. First, a plasmonic film light filter technology is developed. By virtue of enhancing the irradiation of blue and red lights using silver nanospheres and gold nanorods, this technology can enhance microalgal biomass production by up to 50% and increase photosynthetic pigments production by up to 78%. A short light path capable Tris-Acetate-Phosphate-Pluronic (TAPP) microalgal cultivation and harvesting system is also developed. Adding to the interesting light manipulation features, this energy efficient microalgal cultivation and harvesting system that exploits the thermoreversible sol-gel transition properties of the copolymer pluronic can increase the harvesting rate of microalgal biomass via gravimetric sedimentation by a factor of ten. Further, the adhesion properties of microalgal cells on the surface of photobioreactors are studied as a way to control the impacts of biofouling on light penetration and light absorption in microalgal cultivation systems. Furthermore, the rheological properties of microalga C. reinhardtii broths are studied and the interesting properties of such complex fluids are used as tools to control the periodical motion of microalgal cells from dark sections to well illuminated sections of typical photobioreactors for enhanced microalgal growth

Integrating microalgae production with anaerobic digestion: a biorefinery approach

This is the peer reviewed version of the following article: [Uggetti, E. , Sialve, B. , Trably, E. and Steyer, J. (2014), Integrating microalgae production with anaerobic digestion: a biorefinery approach. Biofuels, Bioprod. Bioref, 8: 516-529. doi:10.1002/bbb.1469], which has been published in final form at https://doi.org/10.1002/bbb.1469. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingIn the energy and chemical sectors, alternative production chains should be considered in order to simultaneously reduce the dependence on oil and mitigate climate change. Biomass is probably the only viable alternative to fossil resources for production of liquid transportation fuels and chemicals since, besides fossils, it is one of the only available sources of carbon-rich material on Earth. Over recent years, interest in microalgae biomass has grown in both fundamental and applied research fields. The biorefinery concept includes different technologies able to convert biomass into added-value chemicals, products (food and feed) and biofuels (biodiesel, bioethanol, biohydrogen). As in oil refinery, a biorefinery aims at producing multiple products, maximizing the value derived from differences in biomass components, including microalgae. This paper provides an overview of the various microalgae-derived products, focusing on anaerobic digestion for conversion of microalgal biomass into methane. Special attention is paid to the range of possible inputs for anaerobic digestion (microalgal biomass and microalgal residue after lipid extraction) and the outputs resulting from the process (e.g. biogas and digestate). The strong interest in microalgae anaerobic digestion lies in its ability to mineralize microalgae containing organic nitrogen and phosphorus, resulting in a flux of ammonium and phosphate that can then be used as substrate for growing microalgae or that can be further processed to produce fertilizers. At present, anaerobic digestion outputs can provide nutrients, CO2 and water to cultivate microalgae, which in turn, are used as substrate for methane and fertilizer generation.Peer ReviewedPostprint (author's final draft