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

[EN] 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.The research leading to these results has received funding from the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement number 308518 (CyanoFactory).Gamermann, D.; Montagud Aquino, A.; Conejero Casares, JA.; Urchueguía Schölzel, JF.; Fernández De Córdoba Castellá, PJ. (2014). New approach for phylogenetic tree recovery based on genome-scale metabolic networks. Journal of Computational Biology. 21(7):508-519. https://doi.org/10.1089/cmb.2013.0150S50851921

A transfer matrix method for the analysis of fractal quantum potentials

The scattering properties of quantum particles on fractal potentials at different stages of fractal growth are obtained by means of the transfer matrix method. This approach can be easily adopted for project assignments in introductory quantum mechanics for undergraduates. The reflection coefficients for both the fractal potential and the finite periodic potential are calculated and compared. It is shown that the reflection coefficient for the fractal has a self-similar structure associated with the fractal distribution of the potential

A modular synthetic device to calibrate promoters

In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical model. Our calibrator device possesses certain novel and useful features like modularity (and thus the possibility of being used in many different biological contexts), simplicity, being based on a single cell, high sensitivity and fast response. To uncover the critical model parameters and the corresponding parameter domain at which the calibrator performance will be optimal, a sensitivity analysis of the model parameters was carried out over a given range of sensing protein concentrations (acting as input). Our analysis suggests that the half saturation constants for repression, sensing and difference in binding cooperativity (Hill coefficients) for repression are the key to the performance of the proposed device. They furthermore are determinant for the sensing speed of the device, showing that it is possible to produce detectable differences in the repression protein concentrations and in turn in the corresponding fluorescence in less than two hours. This analysis paves the way for the design, experimental construction and validation of a new family of functional genetic circuits for the purpose of calibrating promoters.Comment: 24 pages, 11 figure

Polarization instabilities in a two-photon laser

We describe the operating characteristics of a new type of quantum oscillator that is based on a two-photon stimulated emission process. This two-photon laser consists of spin-polarized and laser-driven $^{39}$K atoms placed in a high-finesse transverse-mode-degenerate optical resonator, and produces a beam with a power of $\sim$0.2 $\mu$W at a wavelength of 770 nm. We observe complex dynamical instabilities of the state of polarization of the two-photon laser, which are made possible by the atomic Zeeman degeneracy. We conjecture that the laser could emit polarization-entangled twin beams if this degeneracy is lifted.Comment: Accepted by Physical Review Letters. REVTeX 4 pages, 4 EPS figure

Desarrollo de una plataforma computacional para el modelado metabólico de microorganismos

La Biología Sintética (BS) se centra en el diseño y la construcción de sistemas genéticos artificiales, capaces de desarrollar una función específica después de haber sido introducidos en un sistema vivo. Con el desarrollo de la BS, se observa una nueva generación de bioingenieros que desarrollan complejos circuitos biológicos genéticos con un alto nivel de integración. La mejora de esta disciplina científica tiene por objeto establecer un marco computacional y conceptual que dé asistencia al desarrollo de sistemas biológicos artificiales modulares basándose en una metodología ingenieril y sistemática, para lo que se necesita proveer a la próxima generación de diseñadores en Biología Sintética y a los futuros biotecnólogos e ingenieros biológicos de nuevas herramientas computacionales integradas en un entorno común para el análisis de fenotipos metabólicos, el diseño de nuevos circuitos genéticos complejos y la visualización de mapas metabólicos. Como resultado de esta investigación se obtiene la plataforma Hydra (Hybrid Draw and Routes Analysis), que integra diversas herramientas para el diseño, análisis y visualización de las redes metabólicas.Synthetic biology focuses on the design and construction of artificial genetic systems that are capable of carrying out a specific function after being inserted into a living system. With the development of synthetic biology a new generation of bioengineers has appeared who develop complex, highly integrated genetic biological pathways. The improvement of this scientific discipline aims to establish a computational and conceptual framework that will support the development of modular artificial biological systems based on an engineering and systematic methodology. To achieve this, it will be necessary to provide new integrated computational tools in a common environment for the analysis of metabolic phenotypes, the design of new complex genetic pathways and the visualisation of metabolic maps to the next generation of designers in synthetic biology and future biotechnologists and biological engineers. A result of this research is the Hydra platform (Hybrid Draw and Routes Analysis) that integrates various tools for the design, analysis, and visualisation of metabolic networks.Ciencias Experimentale

Estimation of the light field inside photosynthetic microorganism cultures through Mittag-Leffler functions at depleted light conditions

[EN] Light attenuation within suspensions of photosynthetic microorganisms has been widely described by the Lambert-Beer equation. However, at depths where most of the light has been absorbed by the cells, light decay deviates from the exponential behaviour and shows a lower attenuation than the corresponding from the purely exponential fall. This discrepancy can be modelled through the Mittag-Leffler function, extending Lambert-Beer law via a tuning parameter ¿ that takes into account the attenuation process. In this work, we describe a fractional Lambert-Beer law to estimate light attenuation within cultures of model organism Synechocystis sp. PCC 6803. Indeed, we benchmark the measured light field inside cultures of two different Synechocystis strains, namely the wild-type and the antenna mutant strain called Olive at five different cell densities, with our in silico results. The Mittag-Leffler hyper-parameter ¿ that best fits the data is 0.995, close to the exponential case. One of the most striking results to emerge from this work is that unlike prior literature on the subject, this one provides experimental evidence on the validity of fractional calculus for determining the light field. We show that by applying the fractional Lambert-Beer law for describing light attenuation, we are able to properly model light decay in photosynthetic microorganisms suspensions.This project has received funding from the European Unions Seventh Programme for Research, technological development and demonstration under grant agreement No 308518 CyanoFactory. David Fuente is supported by grant Contratos Predoctorales FPI 2013 of the Universitat Politecnica de Valencia. Carlos Lizama is supported by Programa de Apoyo a la Investigation y Desarrollo (PAID-02-15) de la Universitat Politecnica de Valencia and CONICYT - PIA - Anillo ACT1416Fuente, D.; Lizama, C.; Urchueguía Schölzel, JF.; Conejero, JA. (2018). Estimation of the light field inside photosynthetic microorganism cultures through Mittag-Leffler functions at depleted light conditions. Journal of Quantitative Spectroscopy and Radiative Transfer. 204:23-26. https://doi.org/10.1016/j.jqsrt.2017.08.012S232620

Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis

Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance: Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria. © 2011 Belda et al.The research was funded by the Spanish Ministerio de Ciencia e Innovacion, under grant agreement CIT-010000-2008-5 and by a MICINN (Ministerio de Ciencia e Innovacion) TIN2009-12359 ArtBioCom project. Arnau Montagud acknowledges Generalitat Valenciana grant BFPI/2007/283. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Belda Cuesta, EA.; Pedrola, L.; Peretó Magraner, J.; Martinez Blanch, JF.; Montagud Aquino, A.; Navarro-Peris, E.; Urchueguía Schölzel, JF.... (2011). Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis. PLoS ONE. 6(6):21751-21751. https://doi.org/10.1371/journal.pone.0021751S21751217516

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

<p>Abstract</p> <p>Background</p> <p><it>Synechocystis </it>sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO₂and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of <it>Synechocystis </it>sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the <it>Synechocystis </it>metabolic network.</p> <p>Results</p> <p>We report the most comprehensive metabolic model of <it>Synechocystis </it>sp. PCC6803 available, <it>i</it>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 <it>i</it>Syn669 for stoichiometric analysis by simulating three physiologically relevant growth conditions of <it>Synechocystis </it>sp. PCC6803, and through <it>in silico </it>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, <it>i</it>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.</p> <p>Conclusions</p> <p><it>i</it>Syn669 provides a platform for facilitating the development of cyanobacteria as microbial cell factories.</p

CyanoFactory, a European consortium to develop technologies needed to advance cyanobacteria as chassis for production of chemicals and fuels

CyanoFactory, Design, construction and demonstration of solar biofuel production using novel (photo)synthetic cell factories, was an R&D project developed in response to the European Commission FP7-ENERGY-2012-1 call “Future Emerging Technologies” and the need for significant advances in both new science and technologies to convert solar energy into a fuel. CyanoFactory was an example of “purpose driven” research and development with identified scientific goals and creation of new technologies. The present overview highlights significant outcomes of the project, three years after its successful completion. The scientific progress of CyanoFactory involved: (i) development of a ToolBox for cyanobacterial synthetic biology; (ii) construction of DataWarehouse/Bioinformatics web-based capacities and functions; (iii) improvement of chassis growth, functionality and robustness; (iv) introduction of custom designed genetic constructs into cyanobacteria, (v) improvement of photosynthetic efficiency towards hydrogen production; (vi) biosafety mechanisms; (vii) analyses of the designed cyanobacterial cells to identify bottlenecks with suggestions on further improvements; (viii) metabolic modelling of engineered cells; (ix) development of an efficient laboratory scale photobioreactor unit; and (x) the assembly and experimental performance assessment of a larger (1350 L) outdoor flat panel photobioreactor system during two seasons. CyanoFactory - Custom design and purpose construction of microbial cells for the production of desired products using synthetic biology – aimed to go beyond conventional paths to pursue innovative and high impact goals. CyanoFactory brought together ten leading European partners (universities, research organizations and enterprises) with a common goal – to develop the future technologies in Synthetic biology and Advanced photobioreactors