Pedro Fernández de Córdoba

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

BackgroundSynechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network.ResultsWe report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, i Syn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses elementary building blocks that are needed for cell growth, as well as a detailed stoichiometric representation of photosynthesis. We demonstrate applicability of i Syn669 for stoichiometric analysis by simulating three physiologically relevant growth conditions of Synechocystis sp. PCC6803, and through in silico metabolic engineering simulations that allowed identification of a set of gene knock-out candidates towards enhanced succinate production. Gene essentiality and hydrogen production potential have also been assessed. Furthermore, i Syn669 was used as a transcriptomic data integration scaffold and thereby we found metabolic hot-spots around which gene regulation is dominant during light-shifting growth regimes.Conclusionsi Syn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

Synechocystis sp. PCC6803 is a model cyanobacterium capable of producing biofuels with CO(2) as carbon source and with its metabolism fueled by light, for which it stands as a potential production platform of socio-economic importance. Compilation and characterization of Synechocystis genome-scale metabolic model is a pre-requisite toward achieving a proficient photosynthetic cell factory. To this end, we report iSyn811, an upgraded genome-scale metabolic model of Synechocystis sp. PCC6803 consisting of 956 reactions and accounting for 811 genes. To gain insights into the interplay between flux activities and metabolic physiology, flux coupling analysis was performed for iSyn811 under four different growth conditions, viz., autotrophy, mixotrophy, heterotrophy, and light-activated heterotrophy (LH). Initial steps of carbon acquisition and catabolism formed the versatile center of the flux coupling networks, surrounded by a stable core of pathways leading to biomass building blocks. This analysis identified potential bottlenecks for hydrogen and ethanol production. Integration of transcriptomic data with the Synechocystis flux coupling networks lead to identification of reporter flux coupling pairs and reporter flux coupling groups - regulatory hot spots during metabolic shifts triggered by the availability of light. Overall, flux coupling analysis provided insight into the structural organization of Synechocystis sp. PCC6803 metabolic network toward designing of a photosynthesis-based production platform.

Spatial soliton formation in photonic crystal fibers.

We demonstrate the existence of spatial soliton solutions in photonic crystal fibers (PCFs). These guided localized nonlinear waves appear as a result of the balance between the linear and nonlinear diffraction properties of the inhomogeneous photonic crystal cladding. The spatial soliton is realized self-consistently as the fundamental mode of the effective fiber defined simultaneously by the PCF linear and the self-induced nonlinear refractive indices. It is also shown that the photonic crystal cladding is able to stabilize these solutions, which would be unstable otherwise if the medium was entirely homogeneous.

Vortex solitons in photonic crystal fibers.

We demonstrate the existence of vortex soliton solutions in photonic crystal fibers. We analyze the role played by the photonic crystal fiber defect in the generation of optical vortices. An analytical prediction for the angular dependence of the amplitude and phase of the vortex solution based on group theory is also provided. Furthermore, all the analysis is performed in the non-paraxial regime.

Forward-backward equations for nonlinear propagation in axially invariant optical systems.

We present a general framework to deal with forward and backward components of the electromagnetic field in axially invariant nonlinear optical systems, which include those having any type of linear or nonlinear transverse inhomogeneities. With a minimum amount of approximations, we obtain a system of two first-order equations for forward and backward components, explicitly showing the nonlinear couplings among them. The modal approach used allows for an effective reduction of the dimensionality of the original problem from 3 + 1 (three spatial dimensions plus one time dimension) to 1 + 1 (one spatial dimension plus one frequency dimension). The new equations can be written in a spinor Dirac-like form, out of which conserved quantities can be calculated in an elegant manner. Finally, these equations inherently incorporate spatiotemporal couplings, so that they can be easily particularized to deal with purely temporal or purely spatial effects. Nonlinear forward pulse propagation and nonparaxial evolution of spatial structures are analyzed as examples.

A transfer matrix method for the analysis of fractal quantum potentials

The scattering properties of quantum particles on a sequence of potentials converging towards a fractal one are obtained by means of the transfer matrix method. The reflection coefficients for both the fractal potential and finite periodic potential are calculated and compared. It is shown that the reflection coefficient for the fractal potential has a self-similar structure associated with the fractal distribution of the potential whose degree of self-similarity has been quantified by means of the correlation function.

Experimental and Modeling Analysis of Synechocystis sp. PCC 6803 Growth

Background/Aims: The influence of different parameters such as temperature, irradiance, nitrate concentration, pH, and an external carbon source on Synechocystis PCC 6803 growth was evaluated. Methods: 4.5-ml cuvettes containing 2 ml of culture, a high-throughput system equivalent to batch cultures, were used with gas exchange ensured by the use of a Parafilm™ cover. The effect of the different variables on maximum growth was assessed by a multi-way statistical analysis. Results: Temperature and pH were identified as the key factors. It was observed that Synechocystis cells have a strong influence on the external pH. The optimal growth temperature was 33°C while light-saturating conditions were reached at 40 µE·m–2·s–1. Conclusion: It was demonstrated that Synechocystis exhibits a marked difference in behavior between autotrophic and glucose-based mixotrophic conditions, and that nitrate concentrations did not have a significant influence, probably due to endogenous nitrogen reserves. Furthermore, a dynamic metabolic model of Synechocystis photosynthesis was developed to gain insights on the underlying mechanism enabling this cyanobacterium to control the levels of external pH. The model showed a coupled effect between the increase of the pH and ATP production which in turn allows a higher carbon fixation rate.

Nodal solitons and the nonlinear breaking of discrete symmetry

We present a new type of soliton solutions in nonlinear photonic systems with discrete point-symmetry. These solitons have their origin in a novel mechanism of breaking of discrete symmetry by the presence of nonlinearities. These so-called nodal solitons are characterized by nodal lines determined by the discrete symmetry of the system. Our physical realization of such a system is a 2D nonlinear photonic crystal fiber owning C6v symmetry.

Synechocystis sp. PCC6803 metabolic models for the enhanced production of hydrogen

Abstract In the present economy, difficulties to access energy sources are real drawbacks to maintain our current lifestyle. In fact, increasing interests have been gathered around efficient strategies to use energy sources that do not generate high CO2 titers. Thus, science-funding agencies have invested more resources into research on hydrogen among other biofuels as interesting energy vectors. This article reviews present energy challenges and frames it into the present fuel usage landscape. Different strategies for hydrogen production are explained and evaluated. Focus is on biological hydrogen production; fermentation and photon-fuelled hydrogen production are compared. Mathematical models in biology can be used to assess, explore and design production strategies for industrially relevant metabolites, such as biofuels. We assess the diverse construction and uses of genome-scale metabolic models of cyanobacterium Synechocystis sp. PCC6803 to efficiently obtain biofuels. This organism has been studied as a potential photon-fuelled production platform for its ability to grow from carbon dioxide, water and photons, on simple culture media. Finally, we review studies that propose production strategies to weigh this organism’s viability as a biofuel production platform. Overall, the work presented in this review unveils the industrial capabilities of cyanobacterium Synechocystis sp. PCC6803 to evolve interesting metabolites as a clean biofuel production platform.

Aequorin-expressing yeast emits light under electric control

In this study, we show the use of direct external electrical stimulation of a jellyfish luminescent calcium-activated protein, aequorin, expressed in a transgenic yeast strain. Yeast cultures were electrically stimulated through two electrodes coupled to a standard power generator. Even low (1.5 V) electric pulses triggered a rapid light peak and serial light pulses were obtained after electric pulses were applied periodically, suggesting that the system is re-enacted after a short refraction time. These results open up a new scenario, in the very interphase between synthetic biology and cybernetics, in which complex cellular behavior might be subjected to electrical control.