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Tesis por compendio / [EN] Polyploidy is very common in higher plants and is one of the main forces driving evolution, as it leads to changes that may favor plant adaptation. In citrus, polyploid breeding has provided great advantage, enabling the development of new tetraploid (4x) rootstocks and triploid seedless varieties. Rootstock breeding programs aim to combine the characters of interest in a single genotype to provide the required tolerances to biotic and abiotic constraints. In Spain, the presence of citrus tristeza virus (CTV) and the abundance of calcareous and saline soils limit the number of suitable citrus rootstocks. Citrus breeding has been traditionally carried out by sexual hybridization but this method has limitations which are mainly imposed by their complex reproductive biology and their high heterozygosity. To overcome these restrictions, some breeding programs working at tetraploid level have been initiated to facilitate the development of new citrus rootstock ideotypes. The spontaneous appearance of autotetraploid plants in seedlings of apomictic citrus genotypes brings a relatively simple breeding method, offering the opportunity of evaluating their properties and selecting them as new rootstocks. The impact of genome duplication on citrus is variable between species and remains poorly described. To assess the usefulness of 4x citrus rootstocks it is required to evaluate the effect of genome duplication on stress physiology, tree vigor and agronomical behavior. Citrus protoplast fusion allows the somatic hybridization between sexually incompatible species, leading to combine the whole genomes of parents in a single genotype and adding complementary dominant characters, regardless of parental heterozygosity. The purpose of this thesis was to assess the potential interest of the 4x versions of the main rootstocks used in Spanish citrus industry, which are citrange Carrizo (Citrus sinensis (L.) Osb. × Poncirus trifoliata (L.) Raf.) (CC) and C. macrophylla W. (CM) and describe the anatomical, physiological and molecular determinants of the differences found. Additionally, the characterization of two allotetraploid somatic hybrids obtained by protoplast fusion from these parents was also performed, as a preliminary step for their possible use as rootstocks. Results show that 4xCC has a reducing effect on the size of orange trees without changing the productive efficiency or the fruit quality, effects that might contribute to increase the productivity and facilitate the orchard management. In both rootstocks, genome duplication modified the mineral composition in the leaf of the grafted variety and enhanced the salinity tolerance of seedlings. Boron uptake in excess conditions was reduced in 4xCC when compared to 2x, while this property was not observed in 4xCM. The salt and boron exclusion abilities are associated to lower transpiration rates, reduced root hydraulic conductivity and root anatomical changes observed in 4x roots. However, the ability of 4x CC and CM to cope with iron chlorosis is not different from the 2x genotypes. These 4x rootstocks might therefore provide smaller citrus tress more tolerant to certain stresses, while maintaining the general behavior of the diploid genotype. Furthermore, somatic hybrids differ from each other in their genome composition, indicating that losses and rearrangements of the genetic material occurred during the fusion process. Both inherited the tolerance to stem pitting caused by CTV from CC, are tolerant to iron chlorosis like CM and have a higher tolerance to salinity than CC. Thus, these hybrids have a great potential for Mediterranean citrus industry. The provided knowledge on the effects of genome duplication and somatic hybridization on the anatomy, physiology, agronomic performance and molecular biology of citrus rootstocks will be key for developing breeding programs that aim to address current and future needs of citrus industry. / [ES] La poliploidía es una característica muy común en plantas superiores y actúa como motor evolutivo promoviendo su adaptación. En cítricos, la mejora genética a nivel poliploide agiliza el desarrollo de portainjertos tetraploides (4x) y permite obtener variedades sin semilla triploides. El portainjerto es un elemento fundamental en la citricultura para proporcionar al cultivo la tolerancia a estreses bióticos y abióticos. En España, el alto contenido en caliza y sales de la mayoría de los suelos citrícolas y el virus de la tristeza de los cítricos (CTV) limitan en el número de portainjertos adecuados para el cultivo de cítricos. El desarrollo de nuevos portainjertos tiene como objetivo reunir en un genotipo las características de interés. La hibridación sexual ha sido el método tradicionalmente empleado, aunque en cítricos plantea inconvenientes debido a su compleja biología reproductiva y a su alta heterocigosidad. La autotetraploidía, que aparece espontáneamente en los cítricos apomícticos, posibilita la selección y evaluación de las variantes 4x de cada portainjerto. El efecto de la tetraploidía es variable entre las diferentes especies de cítricos y apenas ha sido descrito. Conocer su influencia sobre la fisiología y morfología de los cítricos permitiría valorar su utilidad agronómica. La alotetraploidía, obtenida mediante fusión de protoplastos, permite hibridar especies sexualmente incompatibles y reunir los genomas completos de los parentales, acumulando sus caracteres dominantes complementarios con independencia de la heterozigosidad. El propósito de ésta tesis ha sido evaluar las variantes 4x de los portainjertos más utilizados en España, citrange Carrizo (Citrus sinensis (L.) Osb. × Poncirus trifoliata (L.) Raf.) (CC) y C. macrophylla (CM) para valorar su utilidad agronómica y describir sus propiedades. Además se han caracterizado dos híbridos alotetraploides obtenidos mediante fusión de protoplastos de CM y CC para valorar su posible utilización como portainjertos para la citricultura mediterránea. La tetraploidía en CC y CM modifica la composición mineral foliar de la variedad injertada y mejora la tolerancia de éstas plantas a la salinidad, mientras que la capacidad de hacer frente a la clorosis férrica no difiere entre ploidías en éstos portainjertos. El portainjerto CC4x ejerce un efecto reductor del tamaño de copa en árboles de naranjo sin modificar su eficiencia productiva ni la calidad del fruto y reduce la absorción y transporte de boro a la variedad injertada en condiciones de exceso, mejorando su tolerancia. La mayor capacidad de exclusión de sales y boro en las plantas 4x se relaciona con su menor transpiración. En CC interviene también en este comportamiento la menor conductancia hidráulica de las raíces 4x inducida por sus modificaciones anatómicas. Los híbridos alotetraploides obtenidos mediante fusión de protoplastos de CC y CM difieren en la composición de su genoma, indicando que se han producido pérdidas puntuales y reorganizaciones durante el proceso de fusión. Ambos reúnen los genomas nucleares parentales, han heredado de CC la tolerancia a las acanaladuras en la madera causadas por CTV, son similares a CM en su tolerancia a la clorosis férrica y manifiestan mayor tolerancia a la salinidad que CC. Por ello, reúnen características de gran interés para la citricultura mediterránea. La evaluación y selección de portainjertos 4x permitiría obtener árboles más pequeños y más tolerantes a ciertos estreses que mantengan el comportamiento general ya conocido de los diploides originales. La reducción del tamaño de copa contribuiría a mejorar el rendimiento productivo y a facilitar el manejo de las plantaciones citrícolas. El conocimiento generado sobre los efectos de la tetraploidización y de la hibridación somática en la anatomía, fisiología, comportamiento agronómico y genética de los portainjertos de cítricos ser / [CA] La poliploïdia és molt comuna en plantes superiors i es un dels principals motors evolutius per promoure canvis que afavoreixen la adaptació. En cítrics, la millora genètica a nivell poliploide ha contribuït agilitzant el desenvolupament de nous portaempelts tetraploides (4x) i de varietats sense llavors triploides. En Espanya, el virus de la tristesa dels cítrics (CTV) i l'alt contingut salí i calcari de la majoria dels sols limiten el numere de portaempelts adequats per al cultiu. La millora de portaempelts de cítrics té l'objectiu de reunir el major numere de característiques d'interés en un únic cultivar. La millora genètica tradicional de cítrics, duta a terme mitjançant hibridació sexual, planteja inconvenients deguts a la seua complexa biologia reproductiva i a l'alta heterocigositat. Per aixó s'han iniciat programes de millora de portaempelts a nivell 4x, amb l'objectiu d'agilitzar el seu desenvolupament. La autotetraploïdia, que apareix de manera espontània en especies apomíctiques de cítrics, permet seleccionar les variants 4x dels portaempelts, com un mètode de millora relativament senzill. L'efecte de la tetraploïdia és variable entre les espècies de cítrics i la seua incidència a penes havia sigut descrita. Conéixer la seua repercussió en la tolerància a estressos i el vigor de l'arbre permetria avaluar la utilitat de les versions 4x de cada portaempelt. D'altra banda, l'al¿lotetraploïdia, obtinguda mitjançant la fusió de protoplastos, possibilita l'obtenció d'híbrids d'espècies sexualment incompatibles i reunir en una sola hibridació els genomes complets de les parentals d'interés, permetent l'addició de caràcters dominants complementaris amb independència de l'heterozigositat dels parentals. La finalitat d'esta tesi ha sigut avaluar les propietats d'interés agronòmic de les variants 4x dels portaempelts més utilitzats en la citricultura española, citrange Carrizo (Citrus sinensis (L.) Osb. × Poncirus trifoliata (L.) Raf.) (CC) i C. macrophylla (CM), per valorar la seua utilitat i descriure els determinants de les diferències trobades. A més a més, s'ha pretés realitzar una caracterització molecular i fisiològica de dos híbrids al¿lotetraploides obtinguts de la fusió de protoplastos de CM i CC, com un pas previ per a la seua possible utilització com a portaempelts. El portaempelt CC4x exerceix un efecte reductor de la grandària de copa en arbres de taronger sense modificar l'eficiència productiva ni la qualitat del fruit. Este caràcter milloraría el rendiment productiu i a facilitaría el maneig de les plantacions citricoles. En els dos portaempelts estudiats, la tetraploïdia modifica la composició mineral foliar de la varietat empeltada i proporciona major tolerancia a la salinitat. En CC, la tetraploïdia redueix l'absorció del boro en excés, metre que esta propietat no s'ha observat en CM4x. La menor absorció del boro i l'exclusió del clorur es troben associades a la menor transpiració, a la reduïda conductivitat hidràulica i a les característiques anatòmiques de les arrels 4x. No obstant això, la tolerancia a la clorosi fèrrica no difereix entre ploidíes en estos portaempelts. La selecció de portaempelts 4x permetria obtenir arbres més menuts i més tolerants a certs estressos que mantenen el comportament ja conegut, de la variant diploide. Per la seua banda, els híbrids somàtics difereixen en la composició del genoma, indicant que s'han produït reorganitzacions i pèrdues puntuals durant el procés de fusió. Els dos han heretat de CC la tolerància a les estries en la fusta provocades per CTV, son tolerants a la clorosi fèrrica com CM i toleren la salinitat millor que CC. Per tot, reuneixen un conjunt de característiques de gran interés potencial per a la citricultura mediterrània. El coneixement generat en esta tesi serà de gran utilitat en els programes de millora basades en necessitats actuals i futures. / Ruiz Valdés, M. (2016). Identificación de caracteres fisiológicos y moleculares para la tolerancia a estreses abióticos en portainjertos de cítricos tetraploides [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/73725 / Compendio

La transition des activités humaines vers des modèles de développement durable pourrait contribuer à mieux s’adapter aux enjeux mondiaux interconnectés comme les changements climatiques, l’insécurité alimentaire, la santé globale, et l’épuisement des ressources. Cette thèse représente l’un des premiers travaux de recherche visant à combiner l’utilisation des saules à croissance rapide (Salix sp.) pour la phytoremédiation avec leur potentiel pour les bioraffineries. La métabolomique non-ciblée utilisée avec des saules dans deux études complémentaires a permis d’acquérir à la fois des connaissances appliquées sur la valorisation des composés extractibles et une compréhension fondamentale des mécanismes de tolérance au sel. Des saules matures, utilisés pour traiter des eaux usées, ont été évalués à travers un processus de transformation allant de la biomasse brute aux rendements finaux (bioéthanol, lignines, composés bioactifs). L’irrigation avec des eaux usées a triplé les rendements en biomasse, avec une augmentation significative du glucane au détriment d’une réduction des extractibles. Ces variations suggèrent l’allocation des ressources pour soutenir la croissance plutôt que les molécules de défense. Un prétraitement par liquide ionique a fractionné la biomasse, une méthode compatible avec des biomasses contaminées et permettant d’obtenir des composantes séparées de grande qualité. La saccharification enzymatique a livré les rendements en bioéthanol tandis qu’un contre-solvant a précipité la lignine brute, avec une efficacité similaire aux saules témoins. Malgré une teneur réduite en extractibles, l’irrigation par les eaux usées a enrichi le profil phytochimique en flavonoïdes et lignans, potentiellement associés aux perturbations causées par l’inondation et la salinité, et ayant de possibles propriétés antimicrobiennes et antioxydantes. En intégrant deux approches vertes, cette étude démontre une augmentation significative des rendements annuels de bioproduits par unité de surface cultivée, renforçant la viabilité économique et la durabilité environnementale de chacune des deux approches prises individuellement. Une seconde étude s’intéresse plus profondément aux mécanismes de tolérance d’un saule face à deux sels abondants, le NaCl et le Na2SO4, la salinisation étant généralement associée à l’utilisation d’eaux usées et fréquente sur de nombreuses terres marginales. Malgré une conductance stomatique réduite, Salix miyabeana a maintenu sa capacité photosynthétique et sa production de biomasse, même à des niveaux élevés de sel. Les cations et anions salins sont gérés différemment par la plante, qui restreint largement l’absorption du Na+ aux racines, alors que le Cl- et le SO42- sont transportés jusque dans les feuilles. Les analyses révèlent une tolérance résultant à la fois de la plasticité des métabolites constitutifs et des métabolites spécialisés associés aux organes. Les réponses nuancées en fonction des organes et des ions indiquent des adaptations spécifiques dans l’allocation du carbone, la production d’antioxydants ou le métabolisme du soufre par exemple. Seulement 3% des métabolites constituaient une réponse généralisée aux deux types de sels, incluant une réduction de saccharides et un enrichissement de composés phénoliques simples, comparativement aux 28% impliqués au total. Le NaCl induit une réduction du métabolisme énergétique à l’échelle de toute la plante, potentiellement combinée au renforcement racinaire par l’augmentation de précurseurs de la lignine et d’antioxydants. À niveaux équivalents d’électroconductivité et de sodium, Na2SO4 induit une perturbation métabolique plus limitée. Même à concentration double de Na2SO4, l’activité métabolique se caractérise par un enrichissement préférentiel, probablement facilité par l’assimilation de l’excès de SO42- en composés organiques plutôt que leur séquestration. Notre étude des ajustements métaboliques complexes des saules, une espèce non-modèle mais d’importance biologique, environnementale et économique, a contribué à approfondir notre compréhension de leur résilience face aux stress abiotiques, informant ainsi les approches de gestion de l'eau et des terres ainsi que les pratiques de production durables. / Transitioning towards sustainable models that harmoniously integrate human activities within natural cycles could address interconnected global challenges such as climate change, social and economic inequalities, food insecurity, global health, and resource depletion. Phytoremediation, leveraging plant-microorganism interactions to mitigate soil and water pollution, offers a potentially efficient and environment-friendly solution, while also being economically viable and socially acceptable. This thesis represents one of the initial efforts to integrate the application of fast-growing willows (Salix sp.) for phytoremediation, capitalizing on their stress tolerance, with its potential for widerange biorefineries, harnessing their high biomass productivity as a renewable resource for bioenergy and bio-based products. Two complementary studies employed untargeted metabolomics to acquire both applied knowledge on the extensive valorization potential of extractable phytochemicals, and fundamental understanding of their salt stress tolerance mechanisms. Mature field-grown willows used for phytofiltration of primary municipal wastewater effluent were comprehensively characterized to assess their biorefinery potential through a complete process, from raw biomass to final bioethanol, lignin, and extractives yields. Wastewater irrigation tripled biomass yield and structural biochemical compound quantification revealed a significant increase in constitutive glucan along with a significant decrease in extractives, suggesting resource investment into growth over specialized defensive compounds. Ionic liquid pretreatment enabled biomass fractionation, chosen for its versatility in recovering multiple highquality streams and its suitability for contaminated biomass. Subsequently, enzymatic saccharification determined the final bioethanol yields, while counter-solvent precipitation recovered crude lignins. Despite a generalized reduction of extractives, wastewater irrigation enriched the extractable phytochemical profile with flavonoids and lignans, potentially associated with flooding, salinity, antimicrobial and antioxidant activities. Wastewater irrigated willows maintained quality and conversion potential, enhancing the annual valorization yields per growing surface, and strengthening the economic viability and environmental sustainability. These results demonstrated mutual benefits of integrating wastewater treatment and biorefineries. A subsequent study investigated Salix miyabeana tolerance and metabolic response to two environmentally abundant salts, NaCl and Na2SO4, considering salinity as a potential consequence of wastewater irrigation. Despite reduced stomatal conductance, willows maintained photosynthetic capacity and biomass productivity even under high soil salinity levels, demonstrating their salt tolerance. Elemental analysis revealed differential fate of salt ions, restricted Na+ absorption in roots, while Cl- and SO4 2- accumulated in aerial parts. Untargeted metabolomics exposed willow’s efficient metabolic plasticity in response to salts, modulating both constitutive and organ-specialized metabolites. Differential organ- and anion-specific responses indicated nuanced adaptation mechanisms, involving adjustments in carbon allocation, antioxidant production, and sulfur metabolism. Only 3% of metabolites constituted a generalized salt stress response, including reduced saccharides alongside enriched simple phenolics, as compared to 28% involved in overall salt response. NaCl triggered plant-wide energy metabolism reduction, potentially coupled with reinforced root structure through increased lignin precursors and antioxidant compounds. At similar soil EC and sodium concentration, Na2SO4 caused lower metabolic disruption, and as Na2SO4 concentration increased, willow was able to support the metabolic enrichment instead of depletion, likely associated with the ability to integrate SO4 2- in sulfur metabolism instead of passive sequestration. Our investigation into the complex metabolic adjustments of willows, a non-model species but of biological, environmental and economic importance, contributed to deepen our understanding of its resilience towards abiotic stresses, further informing effective water and land management approaches as well as sustainable production practices.

<p dir="ltr">Reflectance spectroscopy has been increasingly used in forestry due to its ability to rapidly, efficiently, and non-destructively detect tree stress, enabling timely and cost-effective forest management decisions. This dissertation synthesizes three studies and five experiments to understand and improve our ability to use spectral data to estimate a variety of foliar physiochemical traits and identify spectral responses in multi-stress environments, thus, advancing our understanding and application of hyperspectral data in forest management.</p><p dir="ltr">The first study seeks to refine the hyperspectral approach to monitoring tree stress by selecting optimal wavelength ranges to enhance the estimation of foliar traits, such as CO₂ assimilation rate, specific leaf area, leaf water content, and concentrations of foliar nitrogen, sugars, and gallic acid. The study revealed that model performance varied significantly across the different wavelength ranges tested and consistently, including longer wavelength regions improved trait estimation for all traits modeled. This research also established a framework for discovering novel or previously unknown absorption features associated with functional traits, thereby laying the groundwork for expanded spectral applications. This advancement enables the estimation of diverse foliar traits and facilitates detailed stress detection in trees.</p><p dir="ltr">The second study focuses on assessing the effectiveness of hyperspectral data in estimating foliar functional trait responses to various biotic and abiotic stressors and to differentiate those stressors in black walnut (<i>Juglans nigra </i>L.) and red oak (<i>Quercus rubra</i> L.) seedlings. We demonstrated that spectral data can reliably estimate a wide range of foliar traits, highlighting its potential as a surrogate for reference data in understanding plant responses to stress. This research revealed that spectral leaf predictions can effectively provide stress-specific insights into tree physiochemical responses to biotic and abiotic stressors.</p><p dir="ltr">The third study explores the application of hyperspectral reflectance to identify drought-induced foliar responses in black walnut seedlings during their initial field establishment. Chemometric models developed from greenhouse experiments were applied to spectral data collected in the field to assess their transferability and accuracy in predicting various leaf traits under drought stress. Using only spectral data, we demonstrated that seedlings show distinct spectral responses to past and ongoing drought stress, with varying degrees depending on seed provenances. This research aims to provide practical insights for utilizing spectral analysis in real-world conditions and understanding the challenges of using spectral tools in the field.</p><p dir="ltr">Collectively, this dissertation demonstrates the robust potential of hyperspectral reflectance technology in advancing the monitoring of tree health. By optimizing spectral range selection, reliably estimating tree foliar traits under stress conditions, differentiating various stressors in controlled environments, and effectively detecting current and past drought stress in field conditions, this research offers valuable insights for improving forest health monitoring and management strategies in response to environmental challenges.</p>

Die Tetrapyrrol-Biosynthese der Pflanzen ist ein hoch konservierter Prozess, indem sich die Häm- und Chlorophyllsynthese gemeinsame Syntheseschritte von der 5-Aminolävulinsäure (ALA)- bis hin zur Protoporphyrin IX (Proto)-Bildung teilen. Zur Hämsynthese sind in Arabidopsis thaliana zwei Isoformen der Ferrochelatase (FC) vorhanden, welche die Insertion von Eisenionen in Proto katalysieren. In dieser Arbeit wurden fc1 und fc2 Mutanten analysiert und für Komplementationsversuche mit nativen und modifizierten FC1/FC2-Sequenzen genutzt. Die in der fc1-2 Mutante gestörte Embryonalentwicklung infolge des FC1 Mangels konnte durch Expression eines pFC1::FC1 Genkonstruktes komplementiert werden. Die Expression von FC2 unter dem FC1 Promoter (pFC1::FC2) konnte die fc1-2 Mutante unter Standard-Wachstumsbedingungen vollständig komplementieren, jedoch nicht unter Salzstress. Zusätzlich zu den Komplementationsversuchen der fc1 Mutanten wurde auch eine fc2 Null-Mutante zur Expression der beiden genomischen FC Sequenzen herangezogen, um die spezifischen Funktionen der FC2-Varianten zu untersuchen. Während die pFC1FC2 (fc2/fc2) Pflanzen unter Dauerlicht eine vollständige Komplementation zeigten, konnte unter Kurztagbedingungen nur eine partielle Komplementation beobachtet werden. Versuche geben erste wichtige Hinweise, dass auch FC2 an der Regulation der ALA-Synthese infolge ihrer Interaktion mit PORB beteiligt ist. Dies deutet darauf hin, dass der Häm- und der Chlorophyllzweig eine gemeinsame Regulation der ALA-Synthese teilen, um das Gleichgewicht der TBS zu wahren. Neben der Funktion der FC2 in der Regulation der TBS konnte die vorliegende Arbeit ebenfalls die Rolle der FC2 in der Assemblierung der PSII-LHCII Superkomplexe offenlegen. Basierend auf den Ergebnissen, dieser Studie können Modelle für die funktionale Verteilung der beiden FC-Isoformen in unterschiedlichen Geweben und Entwicklungsstadien, sowie die Funktionen in verschiedenen biologischen Prozessen postuliert werden. / In plants, heme and chlorophyll synthesis share the common synthetic steps from 5- aminolevulinic acid (ALA) formation to Protoporphyrin IX (Proto) production in the conserved Tetrapyrrole biosynthesis (TBS) pathway. Arabidopsis thaliana utilizes two ferrochelatses (FC) to catalyse the insertion of ferrous iron into Proto to yield heme. In this study, the fc1 and fc2 defective mutants have been re-analysed and used for complementation tests with expression of a native or modified FC1/FC2 sequence. The pFC1FC1 (fc1/fc1) complementation plants confirmed that the defective embryo maturation in homozygous fc1-2 seeds is attributed to a lack of FC1. Expression of FC2 under the FC1 promoter contributed to a full complementation of fc1-2 under standard growth conditions, but not under salt stress. A fc2 null mutant has been used to express the two FC genomic sequences to substantiate the specific functions of FC2. Expression of FC2 under its own promoter was able to rescue fc2-2 mutants under both SD and CL conditions. However, pFC2FC1 (fc2/fc2) plants showed a partial complementation under SD condition. Via multiple interaction assays and mutant analyses, this thesis uncovered a mechanism of FC2 action on ALA synthesis regulation via interaction of FC2 and PORB. The results indicate that both branches of heme and chlorophyll synthesis share a common regulation to balance the TBS pathway. Apart from a role of FC2 involved in the regulation of TBS pathway, the presented study also revealed FC2 function in the assembly of the PSII-LHCII supercomplexes. Based on all the results obtained in this study, the functional distribution models of the two FC in different tissues and development stages, as well as diverse biological processes, have been proposed. In addition, to which extent that FC1/FC2 could compensate the function of the other isoform has been discussed.

Biotic stress in the form of viral infection, as well as abiotic salt stress, cause leaves injuries, stomata closure and decreased rate of photosynthesis. These factors lead to the limitation of plant growth and to reduced amount of coenzyme NADPH. However NADPH is an important coenzyme for many metabolic pathways such as synthesis of fatty acids, amino acids and secondary metabolites involved in stress responses. NADPH is also a coenzyme for key enzymes of antioxidant system and for many regulatory enzymes. NADP-dependent enzymes are alternative source of NADPH in plants under stress conditions. In this work, activities of four NADP-dependent enzymes: Glucose-6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49), NADP-isocitrate dehydrogenase (NADP-ICDH, EC 1.1.1.42), NADP-malic enzyme (decarboxylating) (NADP-ME, EC 1.1.1.40) and Shikimate dehydrogenase (SDH, EC 1.1.1.25) were studied. Activities of all these enzymes but SDH increased in leaves of tobacco plants (Nicotiana tabacum L.) infected by PVYNTN , The most sensitive enzymes to viral infection were NADP-ICDH and NADP-ME, whose activity was increased in comparison with control plants 3-fold and 2,4-fold, respectively. Changes in activity of studied enzymes were also determined in plants exposed to viral infection in combination with heat-shock...

The study of cis-regulatory elements (CREs) will allow for increased understanding of regulation and lead to insight regarding the mechanisms governing growth, development, health, and disease. The aim of this study was to characterize the de novo in silico predictions of Arabidopsis CREs. Eight synthetic and 30 native promoter-constructs containing an eGFP/GUS reporter protein were generated for cold, genotoxic, heat, osmotic, and salt stress; the circadian clock; ABA signaling; root and epidermis tissue. Constructs were stably transformed into A. thaliana Col-0 and the effects of the CREs were evaluated by in planta stress or tissue assays using GUS expression levels. Results reveal a novel genotoxic element that specifically directs GUS expression in rosette leaves during genotoxic stress. Results also look promising for novel epidermis and root-specific elements. Results of these assays validate the de novo prediction pipeline's ability to identify novel and known CREs related to abiotic stress.

The study of cis-regulatory elements (CREs) will allow for increased understanding of regulation and lead to insight regarding the mechanisms governing growth, development, health, and disease. The aim of this study was to characterize the de novo in silico predictions of Arabidopsis CREs. Eight synthetic and 30 native promoter-constructs containing an eGFP/GUS reporter protein were generated for cold, genotoxic, heat, osmotic, and salt stress; the circadian clock; ABA signaling; root and epidermis tissue. Constructs were stably transformed into A. thaliana Col-0 and the effects of the CREs were evaluated by in planta stress or tissue assays using GUS expression levels. Results reveal a novel genotoxic element that specifically directs GUS expression in rosette leaves during genotoxic stress. Results also look promising for novel epidermis and root-specific elements. Results of these assays validate the de novo prediction pipeline's ability to identify novel and known CREs related to abiotic stress.

Functional characterization of biochemically-isolated proteins is a central task in the biochemical and genetic description of the biology of cells and tissues. Protein identification by mass spectrometry consists of associating an isolated protein with a specific gene or protein sequence in silico, thus inferring its specific biochemical function based upon previous characterizations of that protein or a similar protein having that sequence identity. By performing this analysis on a large scale in conjunction with biochemical experiments, novel biological knowledge can be developed. The study presented here focuses on mass spectrometry-based proteomics of organisms with unsequenced genomes and corresponding developments in biological sequence database searching with mass spectrometry data. Conventional methods to identify proteins by mass spectrometry analysis have employed proteolytic digestion, fragmentation of resultant peptides, and the correlation of acquired tandem mass spectra with database sequences, relying upon exact matching algorithms; i.e. the analyzed peptide had to previously exist in a database in silico to be identified. One existing sequence-similarity protein identification method was applied (MS BLAST, Shevchenko 2001) and one alternative novel method was developed (MultiTag), for searching protein and EST databases, to enable the recognition of proteins that are generally unrecognizable by conventional softwares but share significant sequence similarity with database entries (~60-90%). These techniques and available database sequences enabled the characterization of the Xenopus laevis microtubule-associated proteome and the Dunaliella salina soluble salt-induced proteome, both organisms with unsequenced genomes and minimal database sequence resources. These sequence-similarity methods extended protein identification capabilities by more than two-fold compared to conventional methods, making existing methods virtually superfluous. The proteomics of Dunaliella salina demonstrated the utility of MS BLAST as an indispensable method for characterization of proteins in organisms with unsequenced genomes, and produced insight into Dunaliella?s inherent resilience to high salinity. The Xenopus study was the first proteomics project to simultaneously use all three central methods of representation for peptide tandem mass spectra for protein identification: sequence tags, amino acids sequences, and mass lists; and it is the largest proteomics study in Xenopus laevis yet completed, which indicated a potential relationship between the mitotic spindle of dividing cells and the protein synthesis machinery. At the beginning of these experiments, the identification of proteins was conceptualized as using ?conventional? versus ?sequence-similarity? techniques, but through the course of experiments, a conceptual shift in understanding occurred along with the techniques developed and employed to encompass variations in mass spectrometry instrumentation, alternative mass spectrum representation forms, and the complexities of database resources, producing a more systematic description and utilization of available resources for the characterization of proteomes by mass spectrometry and advanced informatic approaches. The experiments demonstrated that proteomics technologies are only as powerful in the field of biology as the biochemical experiments are precise and meaningful.

Les marais de l'Ouest ont été gagnés sur les sédiments fluvio-marins par poldérisation débutée dès le moyen âge. Les aménagements hydrauliques avaient, initialement, des objectifs sanitaires et d'élevage. A partir des endiguements, ils ont divisé les territoires en marais mouillés et marais desséchés. Depuis les années 1970 le développement des cultures intensives de céréales a nécessité un rabaissement complémentaire de la nappe par drainage en partie pour augmenter la désalinisation de surface et limiter l’engorgement des sols. Néanmoins, ces territoires restent caractérisés par des nappes proches de la surface. En conséquence les profils hydriques vont être gouvernés par les conditions météorologiques y compris l'évapotranspiration, la pluviométrie, mais également par les remontées capillaires issues d'une nappe salée. D'autre par la nature argileuse des sols et ses propriétés de retrait conditionnent énormément le fonctionnement hydrodynamique et les évolutions de structure.La première partie du travail a été de suivre les évolutions des profils hydriques et de salinité en parcelles non drainées (prairies) et en parcelles drainées (Maïs, Blé, Tournesol). Ces suivis ont été complétés par les mesures des niveaux de nappes et par des mesures tensiométriques via des bougies poreuses implantées à différentes profondeurs. L'objectif final a été de calculer et modéliser les profils de réserve utile (RU) et de RU "résiduelle" utilisable par les plantes. Dans ces systèmes alimentés par les remontées capillaires, le réseau racinaire puise l'eau dans la zone non saturée de surface (vadose) puis dans la zone saturée sous-jacente. La teneur en eau caractéristique de l'interface zone non saturée - zone saturée a été déterminée par analogie entre les chemins d'état de la matrice argileuse le long de sa courbe de retrait et du sol le long de sa courbe de compaction. Les profils de RU résiduelle utilisable par les plantes ont été calculés à partir des profils de teneurs en eau puis comparés aux profils de RU obtenus via les données de station météorologique. Ces profils de RU résiduelle ont pu être écrits sous forme d'équation polynomiale du second degré puis modélisés. Dans cet environnement alimenté par les remontées capillaires, ces profils de RU résiduelles peuvent être modélisés à partir d'un paramètre facilement mesurable en surface qui prend en compte la structure du sol et les conditions météorologique : soit la teneur en eau à 10 cm de profondeur. Cette modélisation reste suffisamment réaliste pour être utilisée comme un outil prédictif face à la pédodiversité et/ou les rendements de culture.A ce travail s'ajoute deux études préliminaires : - les mesures des conductivités thermiques effectives de ces sols par la méthode du fil chaud et leurs modélisations dans les systèmes biphasés : eau - argile et air - argile, mais également pour les systèmes triphasés non saturés : eau - air - argile. Les perspectives sont la modélisation des transferts thermiques et hydriques dans le sol à partir de la surface, - et l'élaboration d'un protocole d'imprégnation-polymérisation des sols argileux humides par des résines de type HEMA. Cette imprégnation permet d'envisager la confection de lames minces dans le matériau argileux induré avec conservation de sa structure initiale humide. Les perspectives sont la pétrographie quantitative à l'interface racine - sol le long de profils verticaux dans les environnements argileux à degrés de saturation et structure évolutives. / The coastal marshlands are territories generally reclaimed on primary fluvio-marine sediments. They result from hydraulic managements and/or polderization which may date from the Middle Ages. Historically these hydraulic managements were built for goals of wholesomeness, breeding and farming. They isolate two territories: the dried marshes and the wet marshes. For the intensive cereal crops the slow drying caused by land reclamation was recently improved by the drainage, in part for increase the depth of desalinization and decrease waterlogging. Nevertheless, these territories remain characterized by shallow ground water of initial salt water. Consequently, the hydric profiles are governed by the meteoric conditions including the Evapotranspiration, the rainfall, but also the capillarity rises from the salt groundwater. Moreover, the clay dominated nature of the soils and their drastic shrinkage properties govern the hydrodynamic functioning and the soil structure behavior.The first part of the work was the monitoring of the water content and salinity profiles in drained cereal crops and in undrained grasslands. These measurements have been completed by the ground water level and tensiometric monitoring. The final goal was the calculation and modeling of the available water capacity (AWC) and plant available water (PAW) profiles. In these systems mainly supplied by the capillarity rises, the root network gets water in the subsurface vadose zone and then in the deeper saturated groundwater zone. The water content characteristic of the interface between the vadose and saturated zone was determined by comparison between the clay material state paths along its shrinkage curve and along its compaction curve. The PAW profiles were calculated from the water content profiles and then compared to the AWC profiles. The PAW profiles have been equated as polynomial second degree equations. In these shallow groundwater environments the PAW profiles have been modeled taking into account an easy measurable surface parameter which includes the soil structure behavior and the meteoric conditions: i.e. the water content measured at 10 cm depth. The PAW modelling remains sufficiently realistic to be used as a tool for farming management. Two preliminary studies were added to this work: - the measurement of effective thermal conductivity of the clayey soils by the transient hot wire method, and the modeling of the effective thermal conductivity of biphasic air-clay and water-clay media, but also triphasic unsaturated air-water-clay media. The prospect is the modeling of thermal and hydric transfer from the surface to the depth. - and the elaboration of a protocol of impregnation - hardening for wet clay dominated soils by HEMA resins. This impregnation allows the making of thin sections in these clay materials with conservation of their initial wet structures. The prospective is the quantitative petrography at the root - clay matrix interface along vertical profiles in clayey soils at different degrees of saturation and different structures.