Philosophiae Doctor - PhD / The role of phenolic acids in mitigating salt stress tolerance have been well documented. However, there are contradicting reports on the effect of exogenously applied phenolic acids on the growth and development of various plants species. A general trend was observed where phenolic acids were shown to inhibit plant growth and development, with the exception of a few documented cases. One of these such cases is presented in this thesis. This study investigates the role of exogenously applied p-coumaric acid (p-CA) on physio-biochemical and molecular responses of chia seedlings under salt stress. This study is divided into three parts. Part one (Chapter 3) focuses on the impact of exogenous p-coumaric acid on the growth and development of chia seedlings. In this section, chia seedlings were supplemented with exogenous p-CA and the various biochemical and plant growth parameters were measured. The results showed that exogenous p-CA enhanced the growth of chia seedlings. An increase in chlorophyll, proline and superoxide oxide contents were also observed in the p-CA treatment relative to the control. We suggested that the increase in chia seedling growth could possibly be via the activation of reactive oxygen species-signalling pathway involving O2− under the control of proline accumulation (Chapter 3). Given the allopathy, nature of p-coumaric acid it is noteworthy that the response observed in this study may be species dependent, as contrasting responses have been reported in other plant species. Part two (Chapter 4) of this study investigates the influence of piperonylic acid (an inhibitor of endogenous p-coumaric acid) on the growth and development of chia seedlings. In trying to illustrate whether p-CA does play a regulatory role in enhancing pseudocereal plant growth, we treated chia seedlings with the irreversible inhibitor of C4H enzyme, to inhibit the biosynthesis of endogenous p-CA. In this section, chia seedlings were treated with piperonylic acid and changes in plant growth, ROS-induced oxidative damage, p-CA content and antioxidant capacity was monitored. Inhibition of endogenous p-CA restricted chia seedling growth by enhancing ROS-induced oxidative damage as seen for increased levels of superoxide, hydrogen peroxide and the extent of lipid peroxidation. Although an increase in antioxidant activity was observed in response to piperonylic acid, this increase was not sufficient to scavenge the ROS molecules to prevent oxidative damage and ultimate cellular death manifested as reduced plant growth. The results presented in this section support our hypothesis that p-CA play an important regulatory role in enhancing chia seedling growth and development as shown in Chapter 3. Part three (Chapter 5) seeks to identify and functionally characterise p-coumaric acid induced putative protein biomarkers under salt stress conditions in chia seedlings. Previous studies have shown that p-CA reversing the negative effect caused by NaCl-induced salt stress. While these studies were able to demonstrate the involvement of p-CA in promoting plant growth under salt stress conditions, they focussed primarily on the physiological aspect, which lacks in-depth biochemical and molecular analysis (ionomic and proteomic data) which could help in detecting the genes/proteins involved in salt stress tolerance mechanisms. A comparative ionomics and proteomic study was conducted, with the aim of elucidating the pivotal roles of essential macro elements and/or key protein markers involved in p-CA induced salt stress tolerance in chia seedlings. With the exception of Na, all the other macro elements were decreased in the salt treatment. Contrary to what was observed for the salt treatment most of the macro elements were increased in the p-CA treatment. However, the addition of exogenous p-CA to salt stressed seedlings showed an increase in essential macro elements such as Mg and Ca which have been shown to play a key role in plant growth and development. In the proteomic analysis we identified 907 proteins associated with shoots across all treatments. Interestingly, only eight proteins were conserved amongst all treatments. A total of 79 proteins were unique to the p-CA, 26 to the combination treatment (NaCl + p-CA) and only two proteins were unique to the salt stress treatment. The unique proteins identified in each of the treatments were functionally characterised to various subcellular compartments and biological processes. Most of the positively identified proteins were localised to the chloroplast and plays key roles in photosynthesis, transportation, stress responses and signal transduction pathways. Moreover, the protein biomarkers identified in this study (especially in the p-CA treatment) are putative candidates for genetic improvement of salt stress tolerance in plants.

No description available.

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

<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>

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.

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.