Quartic Kerr cavity combs: bright and dark solitons.

We theoretically investigate the dynamics, bifurcation structure, and stability of localized states in Kerr cavities driven at the pure fourth-order dispersion point. Both the normal and anomalous group velocity dispersion regimes are analyzed, highlighting the main differences from the standard second-order dispersion case. In the anomalous regime, single and multi-peak localized states exist and are stable over a much wider region of the parameter space. In the normal dispersion regime, stable narrow bright solitons exist. Some of our findings can be understood using a new, to the best of our knowledge, scenario reported here for the spatial eigenvalues, which imposes oscillatory tails to all localized states.

Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942.

The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942.

New approach for phylogenetic tree recovery based on genome-scale metabolic networks.

A wide range of applications and research has been done with genome-scale metabolic models. In this work, we describe an innovative methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this comparison in order to infer evolutionary distances between different organisms. Our methodology allows a quantification of the metabolic differences between different species from a broad range of families and even kingdoms. This quantification is then applied in order to reconstruct phylogenetic trees for sets of various organisms.

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.

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.

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.

Yeast cultures with UCP1 uncoupling activity as a heating device.

Uncoupling proteins (UCPs) are mitochondrial transporters that facilitate controlled dissipation of the proton gradient and thus regulate energetic efficiency. The heat generating capacity of UCP from brown adipose tissue was investigated in yeasts expressing the protein recombinantly under conditions in which the temperature of the growth medium was measured directly. A Liquid Culture Calorimeter (LCC) was built consisting of a thermally isolated culture flask able to keep yeast cultures warm without resorting to additional heating. The exact internal temperature of the cultures was monitored for 24h through a thermocouple connected to a data logger. Under these conditions, significant temperature increases (1 degrees C) in the media were recorded when yeast strains expressing endogenously active UCP1 mutants were grown. This is the first direct evidence, in a eukaryotic microbial model, of a temperature rise associated with uncoupling activity, and could be seen as the first step toward developing a biological heating device.

Vortex transmutation.

Using group theory arguments and numerical simulations, we demonstrate the possibility of changing the vorticity or topological charge of an individual vortex by means of the action of a system possessing a discrete rotational symmetry of finite order. We establish on theoretical grounds a "transmutation pass" determining the conditions for this phenomenon to occur and numerically analyze it in the context of two-dimensional optical lattices. An analogous approach is applicable to the problems of Bose-Einstein condensates in periodic potentials.