Genome scale metabolic modeling reveals the metabolic potential of three Type II methanotrophs of the genus Methylocystis

Producción CientíficaGenome Scale Metabolic Models (GSMMs) of the recently sequenced Methylocystis hirsuta and two other methanotrophs from the genus Methylocystis have been reconstructed. These organisms are Type II methanotrophs with the ability of accumulating Polyhydroxyalkanoates under nutrient limiting conditions. For the first time, GSMMs have been reconstructed for Type II methanotrophs. These models, combined with experimental biomass and PHB yields of Methylocystis hirsuta, allowed elucidating the methane oxidation mechanism by the enzyme pMMO (particulate methane monooxygenase) in these organisms. In contrast to Type I methanotrophs, which use the “direct coupling mechanism”, Type II methanotrophs appear to use the so called “redox arm mechanism”. The utilization of the “redox arm mechanism”, which involves the coupling between methane oxidation and complex I of the respiratory chain, was confirmed by inhibition of complex I with catechol. Utilization of the “redox arm” mechanism leads to lower biomass yields on methane compared to Type I methanotrophs. However, the ability of Type II methanotrophs to redirect high metabolic carbon fluxes towards acetoacetyl-CoA under nitrogen limiting conditions makes these organisms promising platforms for metabolic engineering.Marie Curie grant H2020-MSCA-IF-2016 CH4BioVal (GA nº 750126).Junta de Castilla y León (Ref. Project VA281P18)Ministerio de Ciencia e Innovación (Proyect CLU 2017-09, CTM2015-70442-R

Codon usage variability determines the correlation between proteome and transcriptome fold changes

Background: The availability of high throughput experimental methods has made possible to observe the relationships between proteome and transcirptome. The protein abundances show a positive but weak correlation with the concentrations of their cognate mRNAs. This weak correlation implies that there are other crucial effects involved in the regulation of protein translation, different from the sole availability of mRNA. It is well known that ribosome and tRNA concentrations are sources of variation in protein levels. Thus, by using integrated analysis of omics data, genomic information, transcriptome and proteome, we aim to unravel important variables affecting translation. Results: We identified how much of the variability in the correlation between protein and mRNA concentrations can be attributed to the gene codon frequencies. We propose the hypothesis that the influence of codon frequency is due to the competition of cognate and near-cognate tRNA binding; which in turn is a function of the tRNA concentrations. Transcriptome and proteome data were combined in two analytical steps; first, we used Self-Organizing Maps (SOM) to identify similarities among genes, based on their codon frequencies, grouping them into different clusters; and second, we calculated the variance in the protein mRNA correlation in the sampled genes from each cluster. This procedure is justified within a mathematical framework. Conclusions: With the proposed method we observed that in all the six studied cases most of the variability in the relation protein-transcript could be explained by the variation in codon composition

The effect of temperature during culture enrichment on methanotrophic polyhydroxyalkanoate production

Producción CientíficaClimate change and plastic pollution are likely the most relevant environmental problems of the 21st Century. Thus, one of the most promising solutions to remedy both environmental problems simultaneously is the bioconversion of greenhouse gases, such as methane (CH4), into bioplastics (PHAs). However, the optimization of this bioconversion platform is still required to turn CH4 biotransformation into a cost-effective and cost-competitive process. In this context, the research presented here aimed at elucidating the best temperature culture conditions to enhance both PHA accumulation and methane degradation. Six different enrichments were carried out at 25, 30 and 37 °C using different inocula and methane as the only energy and carbon source. CH4 biodegradation rates, specific growth rates, PHA accumulations and the community structure were characterized. Higher temperatures (30 and 37 °C) increased the PHAs accumulation up to 30% regardless of the inoculum. Moreover, Methylocystis became the dominant genus (∼30% of the total population) regardless of the temperature and inoculum used. This research demonstrated for the first time the fundamental role of temperature in increasing both the accumulation of PHAs and methane abatement during the enrichment of PHA cell-factories from methane, thus enhancing the cost-effectiveness of the process.Ministerio de Economía, Industria y Competitividad, TheEuropean FEDER program and the European Commission (CTM2015-73228-JIN, H2020-MSCA-IF-2016: CH4BioVal-GA:750126 and Red NOVEDAR)

Genome sequence of Methylocystis hirsuta CSC1, a polyhydroxyalkanoate producing methanotroph

Producción CientíficaPolyhydroxyalkanoates (PHAs) are biodegradable plastics that can be produced by some methanotrophic organisms such as those of the genus Methylocystis. This allows the conversion of a detrimental greenhouse gas into an environmentally friendly high added‐value bioproduct. This study presents the genome sequence of Methylocystis hirsuta CSC1 (a high yield PHB producer). The genome comprises 4,213,043 bp in 4 contigs, with the largest contig being 3,776,027 bp long. Two of the other contigs are likely to correspond to large size plasmids. A total of 4,664 coding sequences were annotated, revealing a PHA production cluster, two distinct particulate methane monooxygenases with active catalytic sites, as well as a nitrogen fixation operon and a partial denitrification pathway.Ministerio de Ciencia e Innovación (Proyect CTM2015‐70442‐R)Junta de Castilla y León (programa de apoyo a proyectos de investigación – Ref. Project UIC 71

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

<p>Background:</p> <p>The genome-scale metabolic model of Saccharomyces cerevisiae, first presented in 2003, was the first genome-scale network reconstruction for a eukaryotic organism. Since then continuous efforts have been made in order to improve and expand the yeast metabolic network.</p> <p>Results:</p> <p>Here we present iTO977, a comprehensive genome-scale metabolic model that contains more reactions, metabolites and genes than previous models. The model was constructed based on two earlier reconstructions, namely iIN800 and the consensus network, and then improved and expanded using gap-filling methods and by introducing new reactions and pathways based on studies of the literature and databases. The model was shown to perform well both for growth simulations in different media and gene essentiality analysis for single and double knock-outs. Further, the model was used as a scaffold for integrating transcriptomics, and flux data from four different conditions in order to identify transcriptionally controlled reactions, i.e. reactions that change both in flux and transcription between the compared conditions.</p> <p>Conclusion:</p> <p>We present a new yeast model that represents a comprehensive up-to-date collection of knowledge on yeast metabolism. The model was used for simulating the yeast metabolism under four different growth conditions and experimental data from these four conditions was integrated to the model. The model together with experimental data is a useful tool to identify condition-dependent changes of metabolism between different environmental conditions.</p

Nanosatellites costelation mission: ODEI-C24

Our mission consists in 4 key objectives: Quantify the number of sunspots during the solar maximum, and also characterize their activity and magnetism. Demonstrate the reliability of a mission in LEO orbit, for an effective solar observation. Technology demonstrator: we will take on board an experiment: the PTF (Polymer Filter test in flight ), associated with visible cameras. Investigation of the potential for exploitation of ground space market through the sale of images taken in flight

Characterization of the keratinolytic activity of three streptomyces strains and impact of their co-cultivation on this activity

Producción CientíficaIn this study, we describe the characterization of three efficient chicken feather-degrading Streptomyces bacteria isolated from honeybee samples and assess the impact of their co-cultivation on this activity and antistaphylococcal activity. Streptomyces griseoaurantiacus AD2 was the strain showing the highest keratinolytic activity (4000 U × mL−1), followed by Streptomyces albidoflavus AN1 and Streptomyces drozdowiczii AD1, which both generated approximately 3000 U × mL−1. Moreover, a consortium constituted of these three strains was able to use chicken feathers as its sole nutrient source and growth in such conditions led to a significant increase in antibiotic production. S. griseoaurantiacus AD2 was the only strain that exhibited weak antimicrobial activity against Staphylococcus aureus. UPLC analyses revealed that a significant number of peaks detected in the extracts of co-cultures of the three strains were missing in the extracts of individual cultures. In addition, the production of specialized metabolites, such as undecylprodigiosin and manumycin A, was clearly enhanced in co-culture conditions, in agreement with the results of the antimicrobial bioassays against S. aureus. Our results revealed the benefits of co-cultivation of these bacterial species in terms of metabolic wealth and antibiotic production. Our work could thus contribute to the development of novel microbial-based strategies to valorize keratin waste.Fondo Europeo de Desarrollo Regional (FEDER), (grant TCUE 2021–2023) - (project 067/229111)Unión Europea, H2020-MSCA-IF-2016 - (grant UE-18-VANRESTREP-740080

Análisis, construcción, simulación y sincronización de circuitos electrónicos prototipos de Caos

El proyecto tiene como objetivo el estudio de siete Sistemas Dinámicos, yendo de los que son paradigma de Caos a los más complejos, y sus posibles aplicaciones en comunicaciones privadas, bioingeniería y comunicaciones ópticas. El conjunto de sistemas seleccionados incluye algunos ejemplos paradigmáticos de Dinámicas Caóticas, así como nuevas propuestas, tanto de do sistemas básicos como de un sistema que tiene soluciones más complejas, nunca antes estudiados. Se logrará, de esta manera, realizar un completo recorrido desde los osciladores no-lineales más simples (como el de Van Der Pol), hasta los sistemas de mayor complejidad (como son las dinámicas hipercaóticas). El estudio consiste, en primer lugar, en identificar los métodos de análisis específicos del Caos, que permiten poner de manifiesto su carácter y propiedades (a lo que se dedicará el capítulo 1). Tras ello (Capítulo 2 y 3), se desarrollan, estudian y analizan los sistemas mediante simulaciones numéricas de la dinámica de los citados sistemas utilizando el software matemático MATLAB. En una segunda parte (que abarca la primera mitad del Capítulo 4), se implementan los circuitos electrónicos de los citados sistemas, y se simula su comportamiento mediante un software profesional. En una tercera parte (coincidente con la segunda mitad del Capítulo 4 y el Capítulo 5 completo), se construyen físicamente los sistemas fundamentales y sus extensiones, con el objetivo de caracterizar su comportamiento. Además, se desarrolla una aplicación software con entorno gráfico para el análisis sistemático de las dinámicas objeto de estudio. Finalmente, y con el objetivo de aplicar los Sistemas Dinámicos caóticos tanto a Comunicaciones Seguras como a Bioingeniería, este proyecto presenta un estudio de los citados sistemas para su uso en Comunicaciones Seguras, en el capítulo 6. Por otro lado, el oscilador de Van Der Pol no sólo es un sistema paradigma de Caos por la riqueza de su dinámica caótica, sino también por su interés en la simulación del corazón humano tanto en régimen regular, como en régimen caótico. Este análisis se desarrolla en el Capítulo 3

Demonstration of a heterogeneously integrated III-V/SOI single wavelength tunable laser

A heterogeneously integrated III-V-on-silicon laser is reported, integrating a III-V gain section, a silicon ring resonator for wavelength selection and two silicon Bragg grating reflectors as back and front mirrors. Single wavelength operation with a side mode suppression ratio higher than 45 dB is obtained. An output power up to 10 mW at 20 °C and a thermo-optic wavelength tuning range of 8 nm are achieved. The laser linewidth is found to be 1.7 MHz