Competition may explain the fine-scale spatial patterns and genetic structure of two co-occurring plant congeners

1. The spatial distribution of individual plants within a population and the population’s genetic structure are determined by several factors, like dispersal, reproduction mode or biotic interactions. The role of interspecific interactions in shaping the spatial genetic structure of plant populations remains largely unknown. 2. Species with a common evolutionary history are known to interact more closely with each other than unrelated species due to the greater number of traits they share. We hypothesize that plant interactions may shape the fine genetic structure of closely related congeners. 3. We used spatial statistics (georeferenced design) and molecular techniques (ISSR markers) to understand how two closely related congeners, Thymus vulgaris (widespread species) and T. loscosii (narrow endemic) interact at the local scale. Specific cover, number of individuals of both study species and several community attributes were measured in a 10 × 10 m plot. 4. Both species showed similar levels of genetic variation, but differed in their spatial genetic structure. Thymus vulgaris showed spatial aggregation but no spatial genetic structure, while T. loscosii showed spatial genetic structure (positive genetic autocorrelation) at short distances. The spatial pattern of T. vulgaris’ cover showed significant dissociation with that of T. loscosii. The same was true between the spatial patterns of the cover of T. vulgaris and the abundance of T. loscosii and between the abundance of each species. Most importantly, we found a correlation between the genetic structure of T. loscosii and the abundance of T. vulgaris: T. loscosii plants were genetically more similar when they were surrounded by a similar number of T. vulgaris plants. 5. Synthesis. Our results reveal spatially complex genetic structures of both congeners at small spatial scales. The negative association among the spatial patterns of the two species and the genetic structure found for T. loscosii in relation to the abundance of T. vulgaris indicate that competition between the two species may account for the presence of adapted ecotypes of T. loscosii to the abundance of a competing congeneric species. This suggests that the presence and abundance of close congeners can influence the genetic spatial structure of plant species at fine scales.

Effectiveness of AFLPs and retrotransposon-based markers for the identification of portuguese grapevine cultivars and clones

Grapevine germplasm, including 38 of the main Portuguese cultivars and three foreign cultivars, Pinot Noir, Pinot Blanc and Chasselas, used as a reference, and 37 true-to-type clones from the Alvarinho, Arinto, Loureiro, Moscatel Galego Branco, Trajadura and Vinhão cultivars were studied using AFLP and three retrotransposon-based molecular techniques, IRAP, REMAP and SSAP. To study the retrotransposon-based polymorphisms, 18 primers based on the LTR sequences of Tvv1, Gret1 and Vine-1 were used. In the analysis of 41 cultivars, 517 IRAP, REMAP, AFLP and SSAP fragments were obtained, 83% of which were polymorphic. For IRAP, only the Tvv1Fa primer amplified DNA fragments. In the REMAP analysis, the Tvv1Fa-Ms14 primer combination only produced polymorphic bands, and the Vine-1 primers produced mainly ISSR fragments. The highest number of polymorphic fragments was found for AFLP. Both AFLP and SSAP showed a greater capacity for identifying clones, resulting in 15 and 9 clones identified, respectively. Together, all of the techniques allowed for the identification of 54% of the studied clones, which is an important step in solving one of the challenges that viticulture currently faces.

Nematodes as indicators of the effect of soil fumigants on soil functioning

Debido al futuro incierto de la mayor parte de los fumigantes edáficos usados actualmente en la Unión Europea, que pueden implicar riesgos para la salud humana/animal y el medio ambiente, es necesario desarrollar programas de manejo integrado para el control de plagas de cultivos. Estos programas se incluyen como obligatorios en el Reglamento (EC) No. 1107/2009. De acuerdo con este Reglamento, es obligatoria la evaluación del riesgo asociado al uso de productos fitosanitarios sobre los organismos edáficos no diana y sus funciones, además de llevar a cabo ensayos con diferentes especies indicadoras para obtener datos de toxicidad que puedan ser usados posteriormente en la evaluación de riesgo. Sin embargo, la baja representatividad de algunas de estas especies indicadoras en el área Mediterránea supone una gran limitación. En esta situación, el Panel Científico de Productos Fitosanitarios y sus Residuos de la Autoridad Europea en Seguridad Alimentaria (EFSA), ha señalado la necesidad de modificar los datos ecotoxicológicos requeridos para evaluar los efectos adversos de los productos fitosanitarios de una manera más integrada, incluyendo criterios funcionales y estructurales mediante organismos como bacterias, hongos, protozoos y nematodos. De este modo, la EFSA ha recomendado el uso de los nematodos en la evaluación de la funcionalidad y estructura del suelo. Los nematodos están globalmente distribuidos y son morfológicamente diversos; esto junto con su gran abundancia y diversidad de respuestas a las perturbaciones edáficas, los convierte en indicadores adecuados del estado del suelo. Puesto que los nematodos interaccionan con muchos otros organismos que participan en diferentes eslabones de la red trófica edáfica, jugando papeles importantes en procesos edáficos esenciales en los agroescosistemas, la diversidad de nematodos es, a menudo, usada como indicador biológico de los efectos de las prácticas agrícolas en el estado del suelo. En los últimos años, diferentes índices basados en la comunidad nematológica han facilitado la interpretación de datos complejos sobre la ecología del suelo. Los índices de la red trófica edáfica, basados en la abundancia de grupos funcionales definidos como grupos C-P y grupos tróficos, permiten la evaluación de la funcionalidad de la red trófica edáfica. Por otra parte, la dificultad en la identificación taxonómica de nematodos para explicar su uso limitado como indicadores ecológicos, es ampliamente discutida, y existe cierta controversia en cuanto a la eficacia de los diferentes métodos de identificación de nematodos. Se argumenta que la identificación morfológica es difícil y puede llevar mucho tiempo debido a la falta de expertos especializados, y se afirma que las técnicas moleculares pueden resolver algunas limitaciones de las técnicas morfológicas como la identificación de juveniles. Sin embargo, los métodos de identificación molecular tienen también limitaciones; la mayoría de las bases de datos de secuencias de ADN están fuertemente orientadas hacia los nematodos fitoparásitos, los cuales representan sólo una parte de la comunidad edáfica de nematodos, mientras que hay poca información disponible de nematodos de vida libre a pesar de representar la mayoría de los nematodos edáficos. Este trabajo se centra en el estudio de los efectos de fumigantes edáficos en la funcionalidad del suelo a través del uso de diferentes indicadores basados en la comunidad de nematodos, como los índices de la red trófica, índices de diversidad, abundancia de los taxones más relevantes etc. También se han analizado otros indicadores funcionales relacionados con la supresividad edáfica, el ciclo de nutrientes o la actividad de la microfauna del suelo. En el capítulo 1, la diversidad de nematodos estudiada en una explotación comercial de fresa y sus alrededores durante dos campañas consecutivas en el suroeste español, fue baja en los suelos fumigados con fumigantes químicos ambas campañas y, aunque se observó una recuperación a lo largo de la campaña en la zona tratada, los suelos fumigados mostraron una condición perturbada permanente. La comunidad de nematodos estuvo más asociada al ciclo de nutrientes en la zona sin cultivar que en los suelos cultivados, y se observó poca relación entre la biomasa de las plantas y la estructura de la comunidad de nematodos. Los surcos sin tratar dentro de la zona de cultivo funcionaron como reservorio tanto de nematodos fitoparásitos como beneficiosos; sin embargo estas diferencias entre los surcos y los lomos de cultivo no fueron suficientes para mantener la supresividad edáfica en los surcos. Los suelos tratados fueron menos supresivos que los suelos sin tratar, y se observaron correlaciones positivas entre la supresividad edáfica y la estructura de la red trófica edáfica y la diversidad de nematodos. En el capítulo 2, se evaluaron los efectos de dos pesticidas orgánicos con efecto nematicida y dos nematicidas convencionales sobre las propiedades físico químicas del suelo, la diversidad de nematodos y la biomasa de las plantas en condiciones experimentales en dos tipos de suelo: suelos agrícolas poco diversos y suelos provenientes de una zona de vegetación natural muy diversos. El mayor efecto se observó en el tratamiento con neem, el cual indujo un gran incremento en el número de dauerlarvas en los suelos pobres en nutrientes, mientras que el mismo tratamiento indujo un incremento de poblaciones de nematodos bacterívoros, más estables y menos oportunistas, en los suelos del pinar ricos en materia orgánica. En el capítulo 3, se comparó la eficacia de métodos moleculares (TRFLP, Terminal Restriction Fragment Length Polymorphism) y morfológicos (microscopía de alta resolución) para la identificación de diferentes comunidades denematodos de España e Irlanda. Se compararon estadísticamente las diferencias y similitudes en la diversidad de nematodos, otros indicadores ecológicos y de la red trófica edáfica. Las identificaciones mediante el uso de TRFLP sólo detectó un porcentaje de los taxones presentes en las muestras de suelo identificadas morfológicamente, y los nematodos omnívoros y predadores no fueron detectados molecularmente en nuestro estudio. Los índices calculados en base a los nematodos micróboros mostraron más similitud cuando se identificaron morfológica y molecularmente que los índices basados en grupos tróficos más altos. Nuestros resultados muestran que, al menos con la técnica usada en este estudio, la identificación morfológica de nematodos es una herramienta fiable y más precisa que la identificación molecular, puesto que en general se obtiene una mayor resolución en la identificación de nematodos. En el capítulo 4, se estudiaron también los efectos de los nematicidas químicos sobre la comunidad de nematodos y la biomasa de las plantas en condiciones experimentales de campo, donde se aplicaron en una rotación de cultivo judía-col durante un ciclo de cultivo. Se aplicaron dos tipos de enmiendas orgánicas con el objetivo de mitigar el efecto negativo de los productos fitosanitarios sobre la diversidad edáfica. El efecto de los nematicidas sobre las propiedades del suelo y sobre la comunidad de nematodos fue más agudo que el efecto de las enmiendas. La incorporación de los restos de cosecha al final del ciclo de cultivo de la judía tuvo un gran efecto sobre la comunidad de nematodos, y aunque el número total de nematodos incrementó al final del experimento, se observó una condición perturbada permanente de la red trófica edáfica a lo largo del experimento. ABSTRACT Due to the uncertain future of the soil fumigants most commonly used in the EU, that might involve risks for human/animal health and the environment, there is a need to develop new integrated pest management programs, included as mandatory in the Regulation (EC) No. 1107/2009, to control crop diseases. According to this Regulation, evaluating the risk associated to the use of the plant production products (PPP) on non-target soil fauna and their function, and developing assays with different indicator species to obtain toxicity data to be used in the risk evaluation is mandatory. However, the low representativeness of some of these indicator species in the Mediterranean area is a relevant limitation. In this situation, the Scientific Panel of Plant Protection Products and their Residues of the European Food Safety Authority (EFSA) has pointed out the necessity of modifying the ecotoxicological data set required to evaluate non-target effects of PPP in a more integrated way, including structural and functional endpoints with organism such as bacteria, fungi, protists and nematodes. Thus, EFSA has recommended the use of nematodes in the assessment of the functional and structural features of the soil. Nematodes are globally distributed and morphologically diverse, and due to their high abundance and diversity of responses to soil disturbance, they are suitable indicators of the soil condition. Since nematodes interact with many other organisms as participants in several links of the soil food web, playing important roles in essential soil processes in agroecosystems, nematode diversity is often used as a biological indicator of the effects of agricultural practices on soil condition. In the last years, various indices based on soil nematode assemblages, have facilitated the interpretation of complex soil ecological data. Soil food web indices based on the abundances of functional guilds defined by C-P groups and trophic groups, permit evaluating soil food web functioning. On the other hand, the difficulty of nematode taxonomical identification is commonly argued to explain their limited used as ecological indicators, and there is a certain controversy in terms of the efficacy of various nematode identification methods. It is argued that the morphological identification is difficult and time consuming due to the lack of specialist knowledge, and it is claimed that molecular techniques can solve some limitations of morphological techniques such as the identification of juveniles. Nevertheless, molecular identification methods are limited too, since most of the DNA-based databases are strongly oriented towards plant-parasitic nematodes that represent only a fraction of the soil nematode community, while there is little information available on free-living nematodes, which represent most soil nematodes. This work focuses on the study of the effects of soil fumigants on soil functioning through the use of different indicators based on soil nematode community as soil food web indices, diversity indices, the abundance of more relevant taxa etc. Other functional indicators related to soil suppressiveness, nutrient cycling, or the activity of soil microfauna have been also studied. In chapter 1, nematode diversity assessed in a commercial strawberry farm and its surroundings for two consecutive growing seasons in southern Spain, was low in fumigated soils with chemical pesticides throughout both seasons and, although yearly recovery occurred within the treated fields, fumigated soils showed a permanent perturbed condition. The nematode community was more closely associated to nutrient cycling in the non-cropped than in the cropped soils, and the link between plant biomass and nematode community structure was weak. Non-treated furrows within the treated fields were a reservoir of both beneficial and plant-parasitic nematodes, but such difference between furrows and beds was not enough to maintain more suppressive soil assemblages in the furrows. Treated soils were less suppressive than unmanaged soils, and there was a positive and significant correlation between soil suppressiveness and soil food web structure and diversity. In chapter 2, the effects of two organic pesticides with nematicide effect and two chemical nematicides on soil physicalchemical properties, soil nematode diversity and plant biomass in experimental conditions were assessed in two types of soils: low diversity soils from an agricultural farm, and high diversity soils from a natural vegetation area. The larger effect was observed on the neem treatment, which induced a large boost of dauer juveniles in the nutrient-depleted soil, while the same treatment induced the increase of more stable, less opportunistic, populations of generalist bacterivore nematodes in the pine forest soil, rich in organic matter. In chapter 3, comparison of the efficiency of molecular (TRFLP, Terminal Restriction Fragment Length Polymorphism) and morphological (microscopy at high magnification) identification methods was carried out in different nematode communities from five sites of different land uses in Spain and Ireland. Differences and similarities on nematode diversity and other ecological and soil food web indices assessed by both methods, were statistically compared. Molecular identification with TRFLP only detected a percentage of the taxa present in the soil samples identified morphologically, and omnivores and predators were not detected molecularly in our study. Indices involving microbial feeding nematodes were more similar between identification methods than indices involving higher trophic links. Our results show that, at least with the technique used in this study, identifying nematodes morphologically is a reliable and more precise identification tool than molecular identification, since a higher taxonomic resolution is in general obtained compared to TRFLP. In chapter 4, the effect of chemical nematicides on nematode community descriptors and plant biomass was also studied in field conditions in an experimental area in which dazomet and dimethyl disulfide was applied in a bean-cabbage rotation system for a single season. Organic amendments were incorporated into the soil with the aim of mitigate the negative effect of the pesticides on soil diversity. The effect of the nematicides was much more noticeable than the effect of the amendments on soil properties and nematode community descriptors. The incorporation of bean crop residues into the soil at the end of bean crop cycle affected soil nematode community descriptors to a great extent, and although total number of nematodes increased at the end of the experiment, a permanent perturbed soil food web condition was observed along the experiment.

Techniques to accelerate convergence of stress-controlled molecular dynamics simulations of dislocation motion

Dislocation mobility —the relation between applied stress and dislocation velocity—is an important property to model the mechanical behavior of structural materials. These mobilities reflect the interaction between the dislocation core and the host lattice and, thus, atomistic resolution is required to capture its details. Because the mobility function is multiparametric, its computation is often highly demanding in terms of computational requirements. Optimizing how tractions are applied can be greatly advantageous in accelerating convergence and reducing the overall computational cost of the simulations. In this paper we perform molecular dynamics simulations of ½ 〈1 1 1〉 screw dislocation motion in tungsten using step and linear time functions for applying external stress. We find that linear functions over time scales of the order of 10–20 ps reduce fluctuations and speed up convergence to the steady-state velocity value by up to a factor of two.

A molecular dynamics study of swift heavy ion irradiation of amorphous silica: the role of thermal effects

Irradiation with swift heavy ions (SHI), roughly defined as those having atomic masses larger than 15 and energies exceeding 1 MeV/amu, may lead to significant modification of the irradiated material in a nanometric region around the (straight) ion trajectory (latent tracks). In the case of amorphous silica, SHI irradiation originates nano-tracks of higher density than the virgin material (densification). As a result, the refractive index is increased with respect to that of the surroundings. Moreover, track overlapping leads to continuous amorphous layers that present a significant contrast with respect to the pristine substrate. We have recently demonstrated that SHI irradiation produces a large number of point defects, easily detectable by a number of experimental techniques (work presented in the parallel conference ICDIM). The mechanisms of energy transfer from SHI to the target material have their origin in the high electronic excitation induced in the solid. A number of phenomenological approaches have been employed to describe these mechanisms: coulomb explosion, thermal spike, non-radiative exciton decay, bond weakening. However, a detailed microscopic description is missing due to the difficulty of modeling the time evolution of the electronic excitation. In this work we have employed molecular dynamics (MD) calculations to determine whether the irradiation effects are related to the thermal phenomena described by MD (in the ps domain) or to electronic phenomena (sub-ps domain), e.g., exciton localization. We have carried out simulations of up to 100 ps with large boxes (30x30x8 nm3) using a home-modified version of MDCASK that allows us to define a central hot cylinder (ion track) from which heat flows to the surrounding cold bath (unirradiated sample). We observed that once the cylinder has cooled down, the Si and O coordination numbers are 4 and 2, respectively, as in virgin silica. On the other hand, the density of the (cold) cylinder increases with respect to that of silica and, furthermore, the silica network ring size decreases. Both effects are in agreement with the observed densification. In conclusion, purely thermal effects do not explain the generation of point defects upon irradiation, but they do account for the silica densification.

Preliminary approach to neutron instrument selecction at ESSB-Bilbao based on experience at ISIS molecular spectroscopy group

Collaborative efforts between the Neutronics and Target Design Group at the Instituto de Fusión Nuclear and the Molecular Spectroscopy Group at the ISIS Pulsed Neutron and Muon Source date back to 2012 in the context of the ESS-Bilbao project. The rationale for these joint activities was twofold, namely: to assess the realm of applicability of the low-energy neutron source proposed by ESS-Bilbao - for details; and to explore instrument capabilities for pulsed-neutron techniques in the range 0.05-3 ms, a time range where ESS-Bilbao and ISIS could offer a significant degree of synergy and complementarity. As part of this collaboration, J.P. de Vicente has spent a three-month period within the ISIS Molecular Spectroscopy Group, to gain hands-on experience on the practical aspects of neutron-instrument design and the requisite neutron-transport simulations. To date, these activities have resulted in a joint MEng thesis as well as a number of publications and contributions to national and international conferences. Building upon these previous works, the primary aim of this report is to provide a self-contained discussion of general criteria for instrument selection at ESS-Bilbao, the first accelerator-driven, low-energy neutron source designed in Spain. To this end, Chapter 1 provides a brief overview of the current design parameters of the accelerator and target station. Neutron moderation is covered in Chapter 2, where we take a closer look at two possible target-moderator-reflector configurations and pay special attention to the spectral and temporal characteristics of the resulting neutron pulses. This discussion provides a necessary starting point to assess the operation of ESSB in short- and long-pulse modes. These considerations are further explored in Chapter 3, dealing with the primary characteristics of ESS-Bilbao as a short- or long-pulse facility in terms of accessible dynamic range and spectral resolution. Other practical aspects including background suppression and the use of fast choppers are also discussed. The guiding principles introduced in the first three chapters are put to use in Chapter 4 where we analyse in some detail the capabilities of a small-angle scattering instrument, as well as how specific scientific requirements can be mapped onto the optimal use of ESS-Bilbao for condensed-matter research. Part 2 of the report contains additional supporting documentation, including a description of the ESSB McStas component, a detailed characterisation of moderator response and neutron pulses, and estimates ofparameters associated with the design and operation of neutron choppers. In closing this brief foreword, we wish to thank both ESS-Bilbao and ISIS for their continuing encouragement and support along the way.

Molecular Dynamics Simulations of Couette flow

The first steps towards developing a continuum-molecular coupled simulations techniques are presented, for the purpose of computing macroscopic systems of confined fluids. The idea is to compute the interface wall-fluid by Molecular Dynamics simulations, where Lennard-Jones potential (and others) have been employed for the molecular interactions, so the usual non slip boundary condition is not specified. Instead, a shear rate can be imposed at the wall, which allows to obtain the properties of the wall material by means of an iterative method. The remaining fluid region will be computed by a spectral hp method. We present MD simulations of a Couette flow, and the results of the developed boundary conditions from the wall fluid interaction.

Cycling Dof Factors: Molecular and functional characterization of Arabidopsis thaliana AtCDF3 and tomato (Solanum lycopersicum L.) SlCDF3 in response to abiotic stress

El tomate (Solanum lycopersicum L.) es considerado uno de los cultivos hortícolas de mayor importancia económica en el territorio Español. Sin embargo, su producción está seriamente afectada por condiciones ambientales adversas como, salinidad, sequía y temperaturas extremas. Para resolver los problemas que se presentan en condiciones de estrés, se han empleado una serie de técnicas culturales que disminuyen sus efectos negativos, siendo de gran interés el desarrollo de variedades tolerantes. En este sentido la obtención y análisis de plantas transgénicas, ha supuesto un avance tecnológico, que ha facilitado el estudio y la evaluación de genes seleccionados en relación con la tolerancia al estrés. Estudios recientes han mostrado que el uso de genes reguladores como factores de transcripción (FTs) es una gran herramienta para obtener nuevas variedades de tomate con mayor tolerancia a estreses abióticos. Las proteínas DOF (DNA binding with One Finger) son una familia de FTs específica de plantas (Yangisawa, 2002), que están involucrados en procesos fisiológicos exclusivos de plantas como: asimilación del nitrógeno y fijación del carbono fotosintético, germinación de semilla, metabolismo secundario y respuesta al fotoperiodo pero su preciso rol en la tolerancia a estrés abiótico se desconoce en gran parte. El trabajo descrito en esta tesis tiene como objetivo estudiar genes reguladores tipo DOF para incrementar la tolerancia a estrés abiotico tanto en especies modelo como en tomate. En el primer capítulo de esta tesis se muestra la caracterización funcional del gen CDF3 de Arabidopsis, así como su papel en la respuesta a estrés abiótico y otros procesos del desarrollo. La expresión del gen AtCDF3 es altamente inducido por sequía, temperaturas extremas, salinidad y tratamientos con ácido abscísico (ABA). La línea de inserción T-DNA cdf3-1 es más sensible al estrés por sequía y bajas temperaturas, mientras que líneas transgénicas de Arabidopsis 35S::AtCDF3 aumentan la tolerancia al estrés por sequía, osmótico y bajas temperaturas en comparación con plantas wild-type (WT). Además, estas plantas presentan un incremento en la tasa fotosintética y apertura estomática. El gen AtCDF3 se localiza en el núcleo y que muestran una unión específica al ADN con diferente afinidad a secuencias diana y presentan diversas capacidades de activación transcripcional en ensayos de protoplastos de Arabidopsis. El dominio C-terminal de AtCDF3 es esencial para esta localización y su capacidad activación, la delección de este dominio reduce la tolerancia a sequía en plantas transgénicas 35S::AtCDF3. Análisis por microarray revelan que el AtCDF3 regula un set de genes involucrados en el metabolismo del carbono y nitrógeno. Nuestros resultados demuestran que el gen AtCDF3 juega un doble papel en la regulación de la respuesta a estrés por sequía y bajas temperaturas y en el control del tiempo de floración. En el segundo capítulo de este trabajo se lleva a cabo la identificación de 34 genes Dof en tomate que se pueden clasificar en base a homología de secuencia en cuatro grupos A-D, similares a los descritos en Arabidopsis. Dentro del grupo D se han identificado cinco genes DOF que presentan características similares a los Cycling Dof Factors (CDFs) de Arabidopsis. Estos genes son considerados ortólogos de Arabidopsis CDF1-5, y han sido nombrados como Solanum lycopersicum CDFs o SlCDFs. Los SlCDF1-5 son proteínas nucleares que muestran una unión específica al ADN con diferente afinidad a secuencias diana y presentan diversas capacidades de activación transcripcional in vivo. Análisis de expresión de los genes SlCDF1-5 muestran diferentes patrones de expresión durante el día y son inducidos de forma diferente en respuesta a estrés osmótico, salino, y de altas y bajas temperaturas. Plantas de Arabidopsis que sobre-expresan SlCDF1 y SlCDF3 muestran un incremento de la tolerancia a la sequía y salinidad. Además, de la expresión de varios genes de respuesta estrés como AtCOR15, AtRD29A y AtERD10, son expresados de forma diferente en estas líneas. La sobre-expresión de SlCDF3 en Arabidopsis promueve un retardo en el tiempo de floración a través de la modulación de la expresión de genes que controlan la floración como CONSTANS (CO) y FLOWERING LOCUS T (FT). En general, nuestros datos demuestran que los SlCDFs están asociados a funciones aun no descritas, relacionadas con la tolerancia a estrés abiótico y el control del tiempo de floración a través de la regulación de genes específicos y a un aumento de metabolitos particulares. ABSTRACT Tomato (Solanum lycopersicum L.) is one of the horticultural crops of major economic importance in the Spanish territory. However, its production is being affected by adverse environmental conditions such as salinity, drought and extreme temperatures. To resolve the problems triggered by stress conditions, a number of agricultural techniques that reduce the negative effects of stress are being frequently applied. However, the development of stress tolerant varieties is of a great interest. In this direction, the technological progress in obtaining and analysis of transgenic plants facilitated the study and evaluation of selected genes in relation to stress tolerance. Recent studies have shown that a use of regulatory genes such as transcription factors (TFs) is a great tool to obtain new tomato varieties with greater tolerance to abiotic stresses. The DOF (DNA binding with One Finger) proteins form a family of plant-specific TFs (Yangisawa, 2002) that are involved in the regulation of particular plant processes such as nitrogen assimilation, photosynthetic carbon fixation, seed germination, secondary metabolism and flowering time bur their precise roles in abiotic stress tolerance are largely unknown. The work described in this thesis aims at the study of the DOF type regulatory genes to increase tolerance to abiotic stress in both model species and the tomato. In the first chapter of this thesis, we present molecular characterization of the Arabidopsis CDF3 gene as well as its role in the response to abiotic stress and in other developmental processes. AtCDF3 is highly induced by drought, extreme temperatures, salt and abscisic acid (ABA) treatments. The cdf3-1 T-DNA insertion mutant was more sensitive to drought and low temperature stresses, whereas the AtCDF3 overexpression enhanced the tolerance of transgenic plants to drought, cold and osmotic stress comparing to the wild-type (WT) plants. In addition, these plants exhibit increased photosynthesis rates and stomatal aperture. AtCDF3 is localized in the nuclear region, displays specific binding to the canonical DNA target sequences and has a transcriptional activation activity in Arabidopsis protoplast assays. In addition, the C-terminal domain of AtCDF3 is essential for its localization and activation capabilities and the deletion of this domain significantly reduces the tolerance to drought in transgenic 35S::AtCDF3 overexpressing plants. Microarray analysis revealed that AtCDF3 regulated a set of genes involved in nitrogen and carbon metabolism. Our results demonstrate that AtCDF3 plays dual roles in regulating plant responses to drought and low temperature stress and in control of flowering time in vegetative tissues. In the second chapter this work, we carried out to identification of 34 tomato DOF genes that were classified by sequence similarity into four groups A-D, similar to the situation in Arabidopsis. In the D group we have identified five DOF genes that show similar characteristics to the Cycling Dof Factors (CDFs) of Arabidopsis. These genes were considered orthologous to the Arabidopsis CDF1 - 5 and were named Solanum lycopersicum CDFs or SlCDFs. SlCDF1-5 are nuclear proteins that display specific binding to canonical DNA target sequences and have transcriptional activation capacities in vivo. Expression analysis of SlCDF1-5 genes showed distinct diurnal expression patterns and were differentially induced in response to osmotic, salt and low and high temperature stresses. Arabidopsis plants overexpressing SlCDF1 and SlCDF3 showed increased drought and salt tolerance. In addition, various stress-responsive genes, such as AtCOR15, AtRD29A and AtERD10, were expressed differently in these lines. The overexpression of SlCDF3 in Arabidopsis also results in the late flowering phenotype through the modulation of the expression of flowering control genes such CONSTANS (CO) and FLOWERING LOCUS T (FT). Overall, our data connet SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.

Research on wide-bandgap intermediate band solar cells and development of experimental techniques for their characterization

El trabajo que ha dado lugar a esta Tesis Doctoral se enmarca en la invesitagación en células solares de banda intermedia (IBSCs, por sus siglas en inglés). Se trata de un nuevo concepto de célula solar que ofrece la posibilidad de alcanzar altas eficiencias de conversión fotovoltaica. Hasta ahora, se han demostrado de manera experimental los fundamentos de operación de las IBSCs; sin embargo, esto tan sólo has sido posible en condicines de baja temperatura. El concepto de banda intermedia (IB, por sus siglas en inglés) exige que haya desacoplamiento térmico entre la IB y las bandas de valencia y conducción (VB and CB, respectivamente, por sus siglas en inglés). Los materiales de IB actuales presentan un acoplamiento térmico demasiado fuerte entre la IB y una de las otras dos bandas, lo cual impide el correcto funcionamiento de las IBSCs a temperatura ambiente. En el caso particular de las IBSCs fabricadas con puntos cuánticos (QDs, por sus siglas en inglés) de InAs/GaAs - a día de hoy, la tecnología de IBSC más estudiada - , se produce un rápido intercambio de portadores entre la IB y la CB, por dos motivos: (1) una banda prohibida estrecha (< 0.2 eV) entre la IB y la CB, E^, y (2) la existencia de niveles electrónicos entre ellas. El motivo (1) implica, a su vez, que la máxima eficiencia alcanzable en estos dispositivos es inferior al límite teórico de la IBSC ideal, en la cual E^ = 0.71 eV. En este contexto, nuestro trabajo se centra en el estudio de IBSCs de alto gap (o banda prohibida) fabricadsas con QDs, o lo que es lo mismo, QD-IBSCs de alto gap. Hemos fabricado e investigado experimentalmente los primeros prototipos de QD-IBSC en los que se utiliza AlGaAs o InGaP para albergar QDs de InAs. En ellos demostramos une distribución de gaps mejorada con respecto al caso de InAs/GaAs. En concreto, hemos medido valores de E^ mayores que 0.4 eV. En los prototipos de InAs/AlGaAs, este incremento de E^ viene acompaado de un incremento, en más de 100 meV, de la energía de activación del escape térmico. Además, nuestros dispositivos de InAs/AlGaAs demuestran conversión a la alza de tensión; es decir, la producción de una tensión de circuito abierto mayor que la energía de los fotones (dividida por la carga del electrón) de un haz monocromático incidente, así como la preservación del voltaje a temperaura ambiente bajo iluminación de luz blanca concentrada. Asimismo, analizamos el potencial para detección infrarroja de los materiales de IB. Presentamos un nuevo concepto de fotodetector de infrarrojos, basado en la IB, que hemos llamado: fotodetector de infrarrojos activado ópticamente (OTIP, por sus siglas en inglés). Nuestro novedoso dispositivo se basa en un nuevo pricipio físico que permite que la detección de luz infrarroja sea conmutable (ON y OFF) mediante iluminación externa. Hemos fabricado un OTIP basado en QDs de InAs/AlGaAs con el que demostramos fotodetección, bajo incidencia normal, en el rango 2-6/xm, activada ópticamente por un diodoe emisor de luz de 590 nm. El estudio teórico del mecanismo de detección asistido por la IB en el OTIP nos lleva a poner en cuestión la asunción de quasi-niveles de Fermi planos en la zona de carga del espacio de una célula solar. Apoyados por simuaciones a nivel de dispositivo, demostramos y explicamos por qué esta asunción no es válida en condiciones de corto-circuito e iluminación. También llevamos a cabo estudios experimentales en QD-IBSCs de InAs/AlGaAs con la finalidad de ampliar el conocimiento sobre algunos aspectos de estos dispositivos que no han sido tratados aun. En particular, analizamos el impacto que tiene el uso de capas de disminución de campo (FDLs, por sus siglas en inglés), demostrando su eficiencia para evitar el escape por túnel de portadores desde el QD al material anfitrión. Analizamos la relación existente entre el escape por túnel y la preservación del voltaje, y proponemos las medidas de eficiencia cuántica en función de la tensión como una herramienta útil para evaluar la limitación del voltaje relacionada con el túnel en QD-IBSCs. Además, realizamos medidas de luminiscencia en función de la temperatura en muestras de InAs/GaAs y verificamos que los resltados obtenidos están en coherencia con la separación de los quasi-niveles de Fermi de la IB y la CB a baja temperatura. Con objeto de contribuir a la capacidad de fabricación y caracterización del Instituto de Energía Solar de la Universidad Politécnica de Madrid (IES-UPM), hemos participado en la instalación y puesta en marcha de un reactor de epitaxia de haz molecular (MBE, por sus siglas en inglés) y el desarrollo de un equipo de caracterización de foto y electroluminiscencia. Utilizando dicho reactor MBE, hemos crecido, y posteriormente caracterizado, la primera QD-IBSC enteramente fabricada en el IES-UPM. ABSTRACT The constituent work of this Thesis is framed in the research on intermediate band solar cells (IBSCs). This concept offers the possibility of achieving devices with high photovoltaic-conversion efficiency. Up to now, the fundamentals of operation of IBSCs have been demonstrated experimentally; however, this has only been possible at low temperatures. The intermediate band (IB) concept demands thermal decoupling between the IB and the valence and conduction bands. Stateof- the-art IB materials exhibit a too strong thermal coupling between the IB and one of the other two bands, which prevents the proper operation of IBSCs at room temperature. In the particular case of InAs/GaAs quantum-dot (QD) IBSCs - as of today, the most widely studied IBSC technology - , there exist fast thermal carrier exchange between the IB and the conduction band (CB), for two reasons: (1) a narrow (< 0.2 eV) energy gap between the IB and the CB, EL, and (2) the existence of multiple electronic levels between them. Reason (1) also implies that maximum achievable efficiency is below the theoretical limit for the ideal IBSC, in which EL = 0.71 eV. In this context, our work focuses on the study of wide-bandgap QD-IBSCs. We have fabricated and experimentally investigated the first QD-IBSC prototypes in which AlGaAs or InGaP is the host material for the InAs QDs. We demonstrate an improved bandgap distribution, compared to the InAs/GaAs case, in our wide-bandgap devices. In particular, we have measured values of EL higher than 0.4 eV. In the case of the AlGaAs prototypes, the increase in EL comes with an increase of more than 100 meV of the activation energy of the thermal carrier escape. In addition, in our InAs/AlGaAs devices, we demonstrate voltage up-conversion; i. e., the production of an open-circuit voltage larger than the photon energy (divided by the electron charge) of the incident monochromatic beam, and the achievement of voltage preservation at room temperature under concentrated white-light illumination. We also analyze the potential of an IB material for infrared detection. We present a IB-based new concept of infrared photodetector that we have called the optically triggered infrared photodetector (OTIP). Our novel device is based on a new physical principle that allows the detection of infrared light to be switched ON and OFF by means of an external light. We have fabricated an OTIP based on InAs/AlGaAs QDs with which we demonstrate normal incidence photodetection in the 2-6 /xm range optically triggered by a 590 nm light-emitting diode. The theoretical study of the IB-assisted detection mechanism in the OTIP leads us to questioning the assumption of flat quasi-Fermi levels in the space-charge region of a solar cell. Based on device simulations, we prove and explain why this assumption is not valid under short-circuit and illumination conditions. We perform new experimental studies on InAs/GaAs QD-IBSC prototypes in order to gain knowledge on yet unexplored aspects of the performance of these devices. Specifically, we analyze the impact of the use of field-damping layers, and demonstrate this technique to be efficient for avoiding tunnel carrier escape from the QDs to the host material. We analyze the relationship between tunnel escape and voltage preservation, and propose voltage-dependent quantum efficiency measurements as an useful technique for assessing the tunneling-related limitation to the voltage preservation of QD-IBSC prototypes. Moreover, we perform temperature-dependent luminescence studies on InAs/GaAs samples and verify that the results are consistent with a split of the quasi-Fermi levels for the CB and the IB at low temperature. In order to contribute to the fabrication and characterization capabilities of the Solar Energy Institute of the Universidad Polite´cnica de Madrid (IES-UPM), we have participated in the installation and start-up of an molecular beam epitaxy (MBE) reactor and the development of a photo and electroluminescence characterization set-up. Using the MBE reactor, we have manufactured and characterized the first QD-IBSC fully fabricated at the IES-UPM.