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 European Database of Building Energy Profiles to Support the Design of Ground Source Heat Pumps

[EN] The design of ground source heat pumps is a fundamental step to ensure the high energy efficiency of heat pump systems throughout their operating years. To enhance the diffusion of ground source heat pump systems, two different tools are developed in the H2020 research project named, Cheap GSHPs: A design tool and a decision support system. In both cases, the energy demand of the buildings may not be calculated by the user. The main input data, to evaluate the size of the borehole heat exchangers, is the building energy demand. This paper presents a methodology to correlate energy demand, building typologies, and climatic conditions for different types of residential buildings. Rather than envelope properties, three insulation levels have been considered in different climatic conditions to set up a database of energy profiles. Analyzing European climatic test reference years, 23 locations have been considered. For each location, the overall energy and the mean hourly monthly energy profiles for heating and cooling have been calculated. Pre-calculated profiles are needed to size generation systems and, in particular, ground source heat pumps. For this reason, correlations based on the degree days for heating and cooling demand have been found in order to generalize the results for different buildings. These correlations depend on the Koppen-Geiger climate scale.This work received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 657982.Carnieletto, L.; Badenes Badenes, B.; Belliardi, M.; Bernardi, A.; Graci, S.; Emmi, G.; Urchueguía Schölzel, JF.... (2019). A European Database of Building Energy Profiles to Support the Design of Ground Source Heat Pumps. Energies. 12(13):1-23. https://doi.org/10.3390/en12132496S1231213De Carli, M., Tonon, M., Zarrella, A., & Zecchin, R. (2010). A computational capacity resistance model (CaRM) for vertical ground-coupled heat exchangers. Renewable Energy, 35(7), 1537-1550. doi:10.1016/j.renene.2009.11.034Grossi, I., Dongellini, M., Piazzi, A., & Morini, G. L. (2018). Dynamic modelling and energy performance analysis of an innovative dual-source heat pump system. Applied Thermal Engineering, 142, 745-759. doi:10.1016/j.applthermaleng.2018.07.022Engineering Reference Manual. In EnergyPlus V8.5https://energyplus.net/Sandberg, N. H., Bergsdal, H., & Brattebø, H. (2011). Historical energy analysis of the Norwegian dwelling stock. Building Research & Information, 39(1), 1-15. doi:10.1080/09613218.2010.528186Application of Energy Performance Indicators for Residential Building Stocks Experiences of the EPISCOPE Projecthttp://episcope.eu/fileadmin/episcope/public/docs/reports/EPISCOPE_Indicators_ConceptAndExperiences.pdfGustafsson, M., Dipasquale, C., Poppi, S., Bellini, A., Fedrizzi, R., Bales, C., … Holmberg, S. (2017). Economic and environmental analysis of energy renovation packages for European office buildings. Energy and Buildings, 148, 155-165. doi:10.1016/j.enbuild.2017.04.079De Carli, M., Bernardi, A., Cultrera, M., Dalla Santa, G., Di Bella, A., Emmi, G., … Zarrella, A. (2018). A Database for Climatic Conditions around Europe for Promoting GSHP Solutions. Geosciences, 8(2), 71. doi:10.3390/geosciences8020071Cartalis, C., Synodinou, A., Proedrou, M., Tsangrassoulis, A., & Santamouris, M. (2001). Modifications in energy demand in urban areas as a result of climate changes: an assessment for the southeast Mediterranean region. Energy Conversion and Management, 42(14), 1647-1656. doi:10.1016/s0196-8904(00)00156-4Kottek, M., Grieser, J., Beck, C., Rudolf, B., & Rubel, F. (2006). World Map of the Köppen-Geiger climate classification updated. Meteorologische Zeitschrift, 15(3), 259-263. doi:10.1127/0941-2948/2006/0130Herrera, M., Natarajan, S., Coley, D. A., Kershaw, T., Ramallo-González, A. P., Eames, M., … Wood, M. (2017). A review of current and future weather data for building simulation. Building Services Engineering Research and Technology, 38(5), 602-627. doi:10.1177/0143624417705937Peel, M. C., Finlayson, B. L., & McMahon, T. A. (2007). Updated world map of the Köppen-Geiger climate classification. Hydrology and Earth System Sciences, 11(5), 1633-1644. doi:10.5194/hess-11-1633-2007D’Amico, A., Ciulla, G., Panno, D., & Ferrari, S. (2019). Building energy demand assessment through heating degree days: The importance of a climatic dataset. Applied Energy, 242, 1285-1306. doi:10.1016/j.apenergy.2019.03.167Al-Hadhrami, L. M. (2013). Comprehensive review of cooling and heating degree days characteristics over Kingdom of Saudi Arabia. Renewable and Sustainable Energy Reviews, 27, 305-314. doi:10.1016/j.rser.2013.04.034Degree Days.net-Custom Degree Day Datahttp://www.degreedays.netAnnunziata, E., Frey, M., & Rizzi, F. (2013). Towards nearly zero-energy buildings: The state-of-art of national regulations in Europe. Energy, 57, 125-133. doi:10.1016/j.energy.2012.11.049Principle for Nearly Zero-Energy Buildings, Ecofys Germany GmbHhttp://bpie.eu/documents/BPIE/publications/LR_nZEB%20study.pdfAhern, C., Griffiths, P., & O’Flaherty, M. (2013). State of the Irish housing stock—Modelling the heat losses of Ireland’s existing detached rural housing stock & estimating the benefit of thermal retrofit measures on this stock. Energy Policy, 55, 139-151. doi:10.1016/j.enpol.2012.11.039Kaklauskas, A., Zavadskas, E. K., Raslanas, S., Ginevicius, R., Komka, A., & Malinauskas, P. (2006). Selection of low-e windows in retrofit of public buildings by applying multiple criteria method COPRAS: A Lithuanian case. Energy and Buildings, 38(5), 454-462. doi:10.1016/j.enbuild.2005.08.005Zavadskas, E., Raslanas, S., & Kaklauskas, A. (2008). The selection of effective retrofit scenarios for panel houses in urban neighborhoods based on expected energy savings and increase in market value: The Vilnius case. Energy and Buildings, 40(4), 573-587. doi:10.1016/j.enbuild.2007.04.015Aerts, D., Minnen, J., Glorieux, I., Wouters, I., & Descamps, F. (2014). A method for the identification and modelling of realistic domestic occupancy sequences for building energy demand simulations and peer comparison. Building and Environment, 75, 67-78. doi:10.1016/j.buildenv.2014.01.021Yang, Z., & Becerik-Gerber, B. (2014). The coupled effects of personalized occupancy profile based HVAC schedules and room reassignment on building energy use. Energy and Buildings, 78, 113-122. doi:10.1016/j.enbuild.2014.04.002Richardson, I., Thomson, M., & Infield, D. (2008). A high-resolution domestic building occupancy model for energy demand simulations. Energy and Buildings, 40(8), 1560-1566. doi:10.1016/j.enbuild.2008.02.006Villi, G., Peretti, C., Graci, S., & De Carli, M. (2013). Building leakage analysis and infiltration modelling for an Italian multi-family building. Journal of Building Performance Simulation, 6(2), 98-118. doi:10.1080/19401493.2012.69998

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

Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites

[EN] The use of microorganisms as cell factories frequently requires extensive molecular manipulation. Therefore, the identification of genomic neutral sites for the stable integration of ectopic DNA is required to ensure a successful outcome. Herewe describe the genome mapping and validation of five neutral sites in the chromosome of Synechocystis sp. PCC 6803, foreseeing the use of this cyanobacterium as a photoautotrophic chassis. To evaluate the neutrality of these loci, insertion/deletion mutants were produced, and to assess their functionality, a synthetic green fluorescent reporter module was introduced. The constructed integrative vectors include a BioBrick-compatible multiple cloning site insulated by transcription terminators, constituting robust cloning interfaces for synthetic biology approaches. Moreover, Synechocystis mutants (chassis) ready to receive purpose-built synthetic modules/circuits are also available. This work presents a systematic approach to map and validate chromosomal neutral sites in cyanobacteria, and that can be extended to other organisms.This work was supported by the European Commission through the Seventh Framework Programme, FP7-ENERGY-2012-1-2STAGE-308518 (CyanoFactory), from EU FP6-NEST-2005-Path-SYN project BioModularH2 (contract no. 043340) and from National Funds through Fundacao para a Ciencia e a Tecnologia (FCT) (grants SFRH/BD/36378/2007 to F.P., SFRH/BPD/64095/2009 to C.C.P., SFRH/BPD/74894/2010 to P.O.). We also acknowledge the Engineering and Physical Sciences Research Council (EPSRC) for funding (EP/E036252/1) and The University of Sheffield for Scholarship funding. Funding to pay the Open Access publication charges for this article was provided by the European Commission through the Seventh Framework Programme, FP7-ENERGY-2012-1-2STAGE-308518 (CyanoFactory).Pinto, F.; Pacheco, CC.; Oliveira, P.; Montagud, A.; Landels, A.; Couto, N.; Wright, PC.... (2015). Improving a Synechocystis-based photoautotrophic chassis through systematic genome mapping and validation of neutral sites. DNA Research. 22(6):425-437. https://doi.org/10.1093/dnares/dsv024S42543722

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

Introduction to Synthetic Biology

<p>Textbook for a course on Introduction to Synthetic Biology</p