Experimental study of premixed gasoline surrogates burning velocities in a spherical combustion bomb at engine like conditions

Producción CientíficaIn this work are presented experimental values of the burning velocity of iso-octane/air, n-heptane/air and n-heptane/toluene/air mixtures, gasoline surrogates valid over a range of pressures and temperatures similar to those obtained in internal combustion engines. The present work is based on a method to determine the burning velocities of liquid fuels in a spherical constant volume combustion bomb, in which the initial conditions of pressure, temperature and fuel/air equivalence ratios can be accurately established. A two-zone thermodynamic diagnostic model was used to analyze the combustion pressure trace and calculate thermodynamic variables that cannot be directly measured: the burning velocity and mass burning rate. This experimental facility has been used and validated before for the determination of the burning velocity of gaseous fuels and it is validated in this work for liquid fuels. The values obtained for the burning velocity are expressed as power laws of the pressure, temperature and equivalence ratio. Iso-octane, n-heptane and mixtures of n-heptane/toluene have been used as surrogates, with toluene accounting for the aromatic part of the fuel. Initially, the method is validated for liquid fuels by determining the burning velocity of iso-octane and then comparing the results with those corresponding in the literature. Following, the burning velocity of n-heptane and a blend of 50% n-heptane and 50% toluene are determined. Results of the burning velocities of iso-octane have been obtained for pressures between 0.1 and 0.5 MPa and temperatures between 360 and 450 K, for n-heptane 0.1–1.2 MPa and 370–650 K, and for the mixture of 50% n-heptane/50% toluene 0.2–1.0 MPa and 360–700 K. The power law correlations obtained with the results for the three different fuels show a positive dependence with the initial temperature and the equivalence ratio, and an inverse dependence with the initial pressure. Finally, the comparison of the burning velocity results of iso-octane and n-heptane with those obtained in the literature show a good agreement, validating the method used. Analytical expressions of burning velocity as power laws of pressure and unburned temperature are presented for each fuel and equivalence ratio.Ministerio de Ciencia e Innovación (PID2019-106957RB-C22

Combustion and Flame Front Morphology Characterization of H2–CO Syngas Blends in Constant Volume Combustion Bombs

Producción CientíficaThe need to develop new, alternative, and bio-origin fuels for use in internal combustion engines has motivated the realization of this research, which aims to characterize the combustion process synthesis gas, represented by H2–CO blends, which are its main constituents. Syngas can be considered a biofuel because it is a mixture of carbon monoxide, hydrogen, and other hydrocarbons, and it is formed by partial combustion of biomass. Experimental tests have been developed in two constant volume combustion bombs with spherical and cylindrical geometries to analyze the combustion process and the influence of the blend composition on the burning velocity. In the first one, the pressure registered during the combustion has been used to obtain the mass burning rate, temperatures, and burning velocities. The cylindrical bomb has two optical accesses through which the combustion process can be visualized and recorded with the Schlieren technique, and it has been used to characterize the morphology of the flame, the evolution of the flame front, or the laminar burning velocities, among other parameters of interest in the combustion process. For initial conditions of 0.1 MPa and 300 K, blends with different compositions and equivalence ratios have been studied. The introduction of hydrogen enhances combustion velocity and pressure, introducing also instabilities visible on flame front images, similar effects to those produced by increasing the equivalence ratio. Regarding the morphology of the flames, note that the tend to wrinkle and the cellularity increases as the hydrogen content of the mixture increases and the equivalence ratio decreases. The dependence of the numerical values of burning velocity has been expressed as a correlation on pressure and temperature. Finally, comparing the results of the burning velocities obtained in the spherical bomb and in the cylindrical bomb with those of different authors of the bibliography has checked the consistency and validity of them. Results of syngas blends are essential for the validation, optimization, and development of kinetic models for combustion development.Ministerio de Ciencia, Innovación y Universidades - Agencia Estatal de Investigación (grant PID2019-106957RB-C22

MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family

<p>Abstract</p> <p>Background</p> <p>In the past few years, functional genomics information has been rapidly accumulating on Rubiaceae species and especially on those belonging to the <it>Coffea </it>genus (coffee trees). An increasing number of expressed sequence tag (EST) data and EST- or genomic-derived microsatellite markers have been generated, together with Conserved Ortholog Set (COS) markers. This considerably facilitates comparative genomics or map-based genetic studies through the common use of orthologous loci across different species. Similar genomic information is available for e.g. tomato or potato, members of the Solanaceae family. Since both Rubiaceae and Solanaceae belong to the Euasterids I (lamiids) integration of information on genetic markers would be possible and lead to more efficient analyses and discovery of key loci involved in important traits such as fruit development, quality, and maturation, or adaptation. Our goal was to develop a comprehensive web data source for integrated information on validated orthologous markers in Rubiaceae.</p> <p>Description</p> <p>MoccaDB is an online MySQL-PHP driven relational database that houses annotated and/or mapped microsatellite markers in Rubiaceae. In its current release, the database stores 638 markers that have been defined on 259 ESTs and 379 genomic sequences. Marker information was retrieved from 11 published works, and completed with original data on 132 microsatellite markers validated in our laboratory. DNA sequences were derived from three <it>Coffea </it>species/hybrids. Microsatellite markers were checked for similarity, <it>in vitro </it>tested for cross-amplification and diversity/polymorphism status in up to 38 Rubiaceae species belonging to the Cinchonoideae and Rubioideae subfamilies. Functional annotation was provided and some markers associated with described metabolic pathways were also integrated. Users can search the database for marker, sequence, map or diversity information through multi-option query forms. The retrieved data can be browsed and downloaded, along with protocols used, using a standard web browser. MoccaDB also integrates bioinformatics tools (CMap viewer and local BLAST) and hyperlinks to related external data sources (NCBI GenBank and PubMed, SOL Genomic Network database).</p> <p>Conclusion</p> <p>We believe that MoccaDB will be extremely useful for all researchers working in the areas of comparative and functional genomics and molecular evolution, in general, and population analysis and association mapping of Rubiaceae and Solanaceae species, in particular.</p

Ecological genetic and genomic of divergences events of species complexes in tropical rain forest

Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale.Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation

Génétique écologique et génomique des évènements de divergence chez les complexes d’espèces en forêt tropicale humide

Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale

Experimental Study of Premixed Gasoline Surrogates Burning Velocities in a Spherical Combustion Bomb at Engine Like Conditions

In this work are presented experimental values of the burning velocity of iso-octane/air, n-heptane/air and n-heptane/toluene/air mixtures, gasoline surrogates valid over a range of pressures and temperatures similar to those obtained in internal combustion engines. The present work is based on a method to determine the burning velocities of liquid fuels in a spherical constant volume combustion bomb, in which the initial conditions of pressure, temperature and fuel/air equivalence ratios can be accurately established. A two-zone thermodynamic diagnostic model was used to analyze the combustion pressure trace and calculate thermodynamic variables that cannot be directly measured: the burning velocity and mass burning rate. This experimental facility has been used and validated before for the determination of the burning velocity of gaseous fuels and it is validated in this work for liquid fuels. The values obtained for the burning velocity are expressed as power laws of the pressure, temperature and equivalence ratio. Iso-octane, n-heptane and mixtures of n-heptane/toluene have been used as surrogates, with toluene accounting for the aromatic part of the fuel. Initially, the method is validated for liquid fuels by determining the burning velocity of iso-octane and then comparing the results with those corresponding in the literature. Following, the burning velocity of n-heptane and a blend of 50% n-heptane and 50% toluene are determined. Results of the burning velocities of iso-octane have been obtained for pressures between 0.1 and 0.5 MPa and temperatures between 360 and 450 K, for n-heptane 0.1&ndash;1.2 MPa and 370&ndash;650 K, and for the mixture of 50% n-heptane/50% toluene 0.2&ndash;1.0 MPa and 360&ndash;700 K. The power law correlations obtained with the results for the three different fuels show a positive dependence with the initial temperature and the equivalence ratio, and an inverse dependence with the initial pressure. Finally, the comparison of the burning velocity results of iso-octane and n-heptane with those obtained in the literature show a good agreement, validating the method used. Analytical expressions of burning velocity as power laws of pressure and unburned temperature are presented for each fuel and equivalence ratio

High-throughput transcriptome sequencing and preliminary functional analysis in four Neotropical tree species

[b]Background[/b][br/] [br/] The Amazonian rainforest is predicted to suffer from ongoing environmental changes. Despite the need to evaluate the impact of such changes on tree genetic diversity, we almost entirely lack genomic resources.[br/] [br/] [b]Results[/b][br/] [br/] In this study, we analysed the transcriptome of four tropical tree species (Carapa guianensis, Eperua falcata, Symphonia globulifera and Virola michelii) with contrasting ecological features, belonging to four widespread botanical families (respectively Meliaceae, Fabaceae, Clusiaceae and Myristicaceae). We sequenced cDNA libraries from three organs (leaves, stems, and roots) using 454 pyrosequencing. We have developed an R and bioperl-based bioinformatic procedure for de novo assembly, gene functional annotation and marker discovery. Mismatch identification takes into account single-base quality values as well as the likelihood of false variants as a function of contig depth and number of sequenced chromosomes. Between 17103 (for Symphonia globulifera) and 23390 (for Eperua falcata) contigs were assembled. Organs varied in the numbers of unigenes they apparently express, with higher number in roots. Patterns of gene expression were similar across species, with metabolism of aromatic compounds standing out as an overrepresented gene function. Transcripts corresponding to several gene functions were found to be over- or underrepresented in each organ. We identified between 4434 (for Symphonia globulifera) and 9076 (for Virola surinamensis) well-supported mismatches. The resulting overall mismatch density was comprised between 0.89 (S. globulifera) and 1.05 (V. surinamensis) mismatches/100 bp in variation-containing contigs.[br/] [br/] [b]Conclusion[/b][br/] [br/] The relative representation of gene functions in the four transcriptomes suggests that secondary metabolism may be particularly important in tropical trees. The differential representation of transcripts among tissues suggests differential gene expression, which opens the way to functional studies in these non-model, ecologically important species. We found substantial amounts of mismatches in the four species. These newly identified putative variants are a first step towards acquiring much needed genomic resources for tropical tree species

Data from: Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other understudied groups

Microgeographic local adaptation and ecotype distributions: The role of selective processes on early life‐history traits in sympatric, ecologically divergent Symphonia populations

International audienceTrees are characterized by the large number of seeds they produce. Although most of those seeds will never germinate, plenty will. Of those which germinate, many die young, and eventually, only a minute fraction will grow to adult stage and reproduce. Is this just a random process? Do variations in germination and survival at very young stages rely on variations in adaptations to microgeographic heterogeneity? and do these processes matter at all in determining tree species distribution and abundance?We have studied these questions with the Neotropical Symphonia tree species. In the Guiana shield, Symphonia are represented by at least two sympatric taxa or ecotypes, Symphonia globulifera found almost exclusively in bottomlands, and a yet undescribed more generalist taxon/ecotype, Symphonia sp1. A reciprocal transplantation experiment (510 seeds, 16 conditions) was set up and followed over the course of 6 years to evaluate the survival and performance of individuals from different ecotypes and provenances.Germination, survival, growth, and herbivory showed signs of local adaptation, with some combinations of ecotypes and provenances growing faster and surviving better in their own habitat or provenance region. S. globulifera was strongly penalized when planted outside its home habitat but showed the fastest growth rates when planted in its home habitat, suggesting it is a specialist of a high‐risk high‐gain strategy. Conversely, S. sp1 behaved as a generalist, performing well in a variety of environments.The differential performance of seeds and seedlings in the different habitats matches the known distribution of both ecotypes, indicating that environmental filtering at the very early stages can be a key determinant of tree species distributions, even at the microgeographic level and among very closely related taxa. Furthermore, such differential performance also contributes to explain, in part, the maintenance of the different Symphonia ecotypes living in intimate sympatry despite occasional gene flow

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000x, 450x and 120x sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups