Today’s society strives to eliminate the carbon dioxide (CO2) emissions, which is the main greenhouse gas emitted through anthropogenic activities and contributes to climate change. In this project utilization of CO2 emissions from waste to energy plants to carbohydrates via photocatalytic reduction with water and further carbon coupling reactions is investigated. Two routes for the synthesis of carbohydrates have been investigated. Both methods use photocatalytic reduction of carbon dioxide to methanol and then proceed via different steps to produce carbohydrates or their precursors. The first route uses aldol condensation as the main method for the formation of carbon-carbon bonds and the second route is based on the formose reaction that uses formaldehyde as a reactant. The waste incineration plant selected for this study was the one located in Kil, Sweden. This plant processes 15590 tons of waste per year and emits 16366.5 tons of carbon dioxide per year. In order to separate carbon dioxide from the flue gas stream, MEA absorption was chosen as the best option due to its high efficiency. The presented processes have negative carbon dioxide emissions due to the fact that they convert of 16.4% of the waste incineration CO2 emissions into useful products and do not generate any emissions of their own. The aldol condensation pathway exhibits an efficiency of 1.3% when considering only food industry products and 2.5% when including other products that are useful to manufacture solvents, lubricants, or pharmaceuticals. The total amount of food industry products obtained is 3.9 kg/h with the energy requirements being was 159550 kJ/kgproduct. The formose reaction route yields 15.4 kg/h of only food industry products, mainly glucose, and exhibits an efficiency of 5%. The power requirements equal to 90099 kJ/kgproduct. The formose route was found to have higher yield and efficiency, and to be more energy consuming but also more energy efficient. Economic data was difficult to find due to the fact that photocatalytic processes are not commercial yet. / Dagens samhälle strävar efter att eliminera koldioxidutsläppen (CO2), som är den viktigaste växthusgasen som släpps ut genom antropogena aktiviteter och påverkar klimat. Den här projekten undersöker användning av koldioxidutsläpp från avfall till energianläggningar till produktion av kolhydrater via fotokatalytisk reduktion med vatten och ytterligare kolkopplingsreaktioner. Projekten utforskar två vägar för syntes av kolhydrater. Båda metoderna använda fotokatalytisk reduktion av koldioxid till metanol. Kolhydrater eller deras ursprungsmaterial syntetiseras via olika steg nedströms den fotokatalitiska processen. Den första vägen använder aldolkondensation som huvudmetod av kol-kolbindningar och den andra vägen baseras på formosreaktionen som använder formaldehyd som reaktant. Den avfallsförbränningsanläggning som valts ut för denna studie var den i Kil, Värmland, Sverige. Denna anläggning behandlar 15590 ton avfall per år och släpper ut 16366,5 ton koldioxid per år. För att separera koldioxid från rökgasströmmen valdes MEA-absorption som det bästa alternativet på grund av dess höga effektivitet. De presenterade processerna har negativa koldioxidutsläpp på grund av att de omvandlar 16,4% av koldioxid från avfallsförbränning till användbara produkter och inte genererar  egna utsläpp. Aldolkondensationsvägen uppvisar en effektivitet på 1,3% om man endast beaktar livsmedelsindustrins produkter och 2,5% om man gör andra produkter som är användbara för att tillverka lösningsmedel, smörjmedel eller läkemedel. Den totala mängden av livsmedelsprodukter är 3,9 kg / h och energibehovet är lika med 159550 kJ / kg produkt. Formosreaktionsvägen ger 15,4 kg / h av livsmedelsindustrin produkt, huvudsakligen glukos, och uppvisar en effektivitet på 5%. Effektkraven är lika med 90099 kJ / kg produkt. Formosvägen visade sig ha högre utbyte och effektivitet och vara mer energikrävande men också mer energieffektiv. Ekonomiska data var svåra att hitta på grund av att fotokatalytiska processorn ännu inte är kommersiell.

<p dir="ltr">Photosynthesis is the basis of primary productivity on Earth. Oxygenic photosynthesis utilizes the nearly inexhaustible energy of radiant solar light to fix atmospheric carbon dioxide into usable forms of chemical energy and produces dioxygen as a product. Central to this process are several large hetero-oligomeric protein complexes that comprise the photosynthetic electron transport chain. Photosystem II (PSII) initiates electron transport through the light-driven oxidation of water, in-turn relinquishing protons and oxygen. Through this reaction, electrons are used to form the reductant NADPH, while protons form a proton-motive gradient that is used to drive synthesis of ATP. As a result of this highly energetic reaction, PSII is often subject to oxidative photodamage due to the production of reactive oxygen species. Inevitably, accumulation of oxidative photodamage disrupts the catalytic activity of PSII, resulting in a loss of photosynthetic activity. To deal with the nearly constant incurred photodamage to PSII, oxygenic photoautotrophs undergo a disassembly and repair cycle that results in the complete turnover of the damaged D1 subunit of PSII. Due to its high tendency for damage, the D1 subunit has a half-life of under one hour in high light intensity. Despite our current understanding of photoinhibition and PSII repair, it is still unclear how D1 is replaced so rapidly in response to damaging conditions. Previous research has indicated a role for phosphorylation of PSII in D1 turnover, however the mechanism has not been totally resolved. In the first chapter of this thesis, our current understanding of PSII phosphorylation and oxidative damage is reviewed in the context of PSII repair. In the second chapter, the role of protein phosphorylation in the PSII repair cycle is investigated in the model organism <i>Arabidopsis</i>. Using several PSII phosphorylation mutants, we demonstrate that phosphorylation seems to mediate disassembly of large PSII supercomplexes and dimers into smaller subcomplexes. In the third chapter, the role of oxidative photodamage is investigated in mediating PSII disassembly. Here, we use several <i>in vitro</i> assays to demonstrate that photodamage is sufficient to induce the disassembly of smaller PSII subcomplexes. In the fourth chapter, a technique for determining the stoichiometry of photosynthetic complexes is examined, with implications for understanding PSII repair. Finally, in the fifth chapter, several conclusions and unanswered questions from this thesis are discussed.</p>

Kolavskiljning, avlägsnande av koldioxid (CO2) från atmosfären, har fått uppmärksamhet som en metod för att mildra effekterna av den globala uppvärmningen. Växter och fototrofa mikroorganismer har den inneboende förmåganatt fånga upp kol genom fixering av CO2 för att producera biomassa. Däremot inhemska kolfixeringsvägar begränsas av nyckelenzymer med låg katalytisk aktivitet vilket resulterar i låg energieffektivitet. Rubisco är en sådan nyckelenzym, ökänt för sin dåliga prestanda. Tidigare forskning har misslyckats när det gäller att förbättra kolet fixering i Rubisco med konventionella metoder. Generativ modellering har dykt upp som en innovativ förhållningssätt till enzymteknik, dra fördel av olika arkitekturer för neurala nätverk för att föreslå en ny varianter med önskade egenskaper. Här tränas en variationsautokodare (VAE) på Rubisco-sekvensen utrymme användes för utmaningen med Rubiscos ingenjörskonst. Två modeller utbildades och med hjälp av dimensionsreduktionsegenskapen hos VAE, utforskades fitnesslandskapet i Rubisco. Sekvenser var märkt med katalytiskt relevanta data och en regressionsmodell byggdes med syftet att förutsäga dessa sekvenser med ökad katalytisk aktivitet. Nya Rubisco-sekvenser genererades efter systematiska utfrågning av det lågdimensionella rummet. Användningen av generativ modellering här ger ett nytt perspektiv på Rubisco engineering. / Carbon capture, the removal of carbon dioxide (CO2) from the atmosphere, has gained attention as a method to mitigate the effects of global warming. Plants and phototrophic microorganisms have the inherent ability to capture carbon through the fixation of CO2 to produce biomass. However, native carbon fixing pathways are limited by key enzymes with low catalytic activity resulting in low energy efficiency. Rubisco is one such key enzyme, notorious for its poor performance. Past research has been unsuccessful at enhancing carbon fixation in Rubisco through conventional methods. Generative modelling has emerged as an innovative approach to enzyme engineering, taking advantage of different neural network architectures to propose novel variants with desired characteristics. Here, a variational autoencoder (VAE) trained on the Rubisco sequence space was applied to the challenge of Rubisco engineering. Two models were trained and, using the dimensionality reduction property of VAEs, the fitness landscape of Rubisco was explored. Sequences were labelled with catalytically relevant data and a regression model was built with the aim of predicting those sequences with enhanced catalytic activity. Novel Rubisco sequences were generated following systematic interrogation of the low-dimensional space. The use of generative modelling here provides a fresh perspective on Rubisco engineering.

Fotosyntes är central för vår överlevnad. I denna studie har en artificel ljuskälla reglerats för att optimera fotonintensiteten då intensiteten från solen varit för låg. Fokus är lagt på PAR-vågbandet vilket är de våglängder som anses ha störst inverkan på fotosyntes. En kalibrerad sensor användes för att ge pålitliga mätvärden av fotonintensiteten. En billig sensor konstruerades för mätning av densamma och även manuell mätning med lux-meter där värdena konverterades till fotonintensitet. För att studera hur tillväxten påverkas av fotonintensiteten har en testgrupp och en kontrollgrupp med morötter används. Morötterna placerades i ett växthus under liknande förutsättningar med avseende på till exempel näring och värme. Testgruppen fick tillgång till artificellt ljus då intensiteten från solen var för låg under dagstid. Kontrollgruppen fick endast tillgång till solljus. Tillväxten för testgruppen blev större än för kontrollgruppen. För vidare forskning skulle en steglös reglering av fotonbombardemanget kunna optimera processen. Denna förbättring innebär ekonomisk besparing i form av högre biologisk tillväxt vid lägre energiförbrukning. Slutsatsen av denna studie är att optimering av fotonbombardemang kan medföra ekonomisk besparing och även minskad negativ miljöpåverkan på grund av lägre energiförbrukning. / Photosynthesis is central to our survival. In this study, an artificial light source has been regulated to optimize the photon intensity when the intensity from the sun has been too low. The focus is on the PAR waveband, which are the wavelengths that are considered to have the greatest impact on photosynthesis. A calibrated sensor was used to provide reliable measurements of the photon intensity. An inexpensive sensor was designed for measuring the same and also manual measurement with lux-meter where the values ​​were converted to photon intensity. To study how growth is affected by photon intensity, a test group and a control group with carrots were used. The carrots were placed in a greenhouse under similar conditions with regard to, for example, nutrition and heat. The test group gained access to artificial light when the intensity from the sun was too low during the day. The control group only had access to sunlight. The growth for the test group was greater than for the control group. For further research, a stepless regulation of photon bombardment could optimize the process. This improvement means economic saving in the form of higher biological growth at lower energy consumption. The conclusion of this study is that optimization of photon bombardment can lead to economic saving and also reduced negative environmental impact due to lower energy consumption.

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: The Southern Ocean (SO) is of significant interest in the understanding of the global carbon cycle and therefore many studies have been conducted to determine the limiting factors controlling the biological pump within the region. During photosynthesis phytoplankton require various nutrients such as NO3, PO4, inorganic carbon and the micronutrient Fe. The SO is a High-Nutrient Low-Chlorophyll region, therefore no macronutrient limitation is experienced by resident phytoplankton but instead the micronutrient Fe is a significant limiting factor within these waters due to limited inputs. Due to deep mixed layer depths, ice cover, low sun angles and cloud cover throughout parts of the year, light is also considered a limiting factor in the SO. Fe and light limitation cause a decrease in photosynthetic efficiency and therefore a decrease in carbon fixation capabilities. During this study we conducted five bioassay shipboard incubation experiments during two cruises along the Greenwich meridian between South Africa and the ice edge, SOSCEx during March and SAFePool during January to February, in which we varied Fe concentrations and light levels to determine the effects of Fe and light limitation or co-limitation within resident phytoplankton. Spatial and temporal variations in phytoplankton response were studied to determine varying effects of limitation across water masses and different stages of bloom decline within the study area. The combined addition of Fe and light gave the largest increase in biomass, photosynthetic capacity and nutrient uptake. In support of the hypotheses tested changes in the photosynthetic apparatus led to changes in the photosynthetic efficiency and growth of the SO phytoplankton, as a result of variations in Fe and light availability. Variability was also observed in the response of phytoplankton to Fe and light amendments due to spatial and temporal variation in resident phytoplankton communities. It was therefore concluded that both Fe and light are significant controls in the resident phytoplankton photosynthetic apparatus, photosynthetic capabilities, organic carbon fixation and therefore the biogeochemical cycles within the Atlantic sector of the SO. / AFRIKAANSE OPSOMMING: Die Suidelike Oseaan (SO) is van beduidende belang in die begrip van die globale koolstofsiklus en dus is baie studies gedoen om die beperkende faktore te bepaal wat die biologiese pomp in die streek beheer. Tydens fotosintese benodig fitoplankton verskillende voedingstowwe soos NO3, PO4, anorganiese koolstof en die mikrovoedingstof Fe. Die SO is 'n High-Nutrient Lae-Chlorofil streek, dus word geen makrovoedingstof beperking ervaar deur inwoner fitoplankton maar in plaas daarvan is die mikrovoedingstof Fe 'n beduidende beperkende faktor binne hierdie waters weens beperkte insette. As gevolg van diep gemengde laag dieptes, ysbedekking, lae son hoeke en wolkbedekking deur dele van die jaar, word lig ook beskou as 'n beperkende faktor in die SO. Fe en lig beperking veroorsaak 'n afname in die fotosintetiese doeltreffendheid en dus 'n afname in koolstof binding vermoëns. Tydens hierdie studie het ons vyf biotoets inkubasie eksperimente aan boord die skeep gedoen tydens twee vaarte langs die Greenwich meridiaan tussen Suid-Afrika en die ys rand, SOSCEx gedurende Maart en SAFePool gedurende Januarie tot Februarie, waarin ons Fe konsentrasies en lig vlakke gewissel het om die gevolge van Fe en lig beperking, of medebeperking, binne inwoner fitoplankton te bepaal. Ruimtelike en temporale variasies in fitoplankton reaksie was bestudeer om wisselende gevolge van die beperking oor watermassas en verskillende stadiums van bloei afname in die studie area te bepaal. Die gekombineerde byvoeging van Fe en lig het die grootste toename in biomassa, fotosintetiese kapasiteit en voedingsopname gegee. Ter ondersteuning van die getoetste hipoteses, veranderinge in die fotosintetiese apparaat het gelei tot veranderinge in die fotosintetiese doeltreffendheid en groei van die SO fitoplankton, as 'n gevolg van variasies in Fe en lig beskikbaarheid. Veranderlikheid is ook waargeneem in die reaksie van fitoplankton om Fe en lig wysigings weens die ruimtelike en tydelike variasie in inwoner fitoplankton gemeenskappe. Dus was dit by die gevolgtrekking gekom dat beide Fe en lig beduidende kontrole in die inwoner fitoplankton fotosintetiese apparaat, fotosintetiese vermoëns, organiese koolstof binding en daarom die biogeochemiese siklusse binne die Atlantiese sektor van die SO.

The main aim of this study was to investigate the effects of water availability and SO2 pollution, imposed separately or simultaneously, on the photosynthetic metabolism of Augea capensis Thunb., a succulent of the Namib Desert in the region of Skorpion Zinc mine, Namibia. The main driver for this investigation was the need to distinguish between the effects of water availability on plants native to a desert environment, where water availability dominates plant response, but where the possibility of anthropogenic SO2 pollution poses a new threat to the unique succulent vegetation. Fifteen measuring sites were selected in the vicinity of the mine to determine how rainfall influenced the physiological status of the vegetation. Chlorophyll a fluorescence measurements, and analysis of recorded OJlP fluorescence transients with the JIP-test, were used for this purpose. A series of laboratory experiments were also conducted on A. capensis to determine the precise physiological response that water deprivation and SO2 pollution had under controlled growth conditions. Potted plants were exposed to water deprivation or SO2 fumigation in the light or dark. Besides chlorophyll a fluorescence, photosynthetic gas exchange and Rubisco activity were also measured. Changes in fast fluorescence rise kinetics observed under field conditions suggest considerable modulation of photosystem II function by rainfall with concomitant involvement of a heat stress component as well. In both the field and laboratory experiments, one of the JIP-test parameters, the so-called performance index (PIABS), was identified as a very sensitive indicator of the physiological status of the test plants. Moreover, under laboratory conditions, a good correlation existed between the water deprivation-induced decline in CO2 assimilation rates and the decline in PIABS values. The JIP-test in general, and the PIABS in particular, shows considerable potential for application in the investigation of water availability influences on desert ecosystems. In the laboratory experiments, water deprivation caused stomatal closure but also a slight elevation in intercellular C02 concentration and inhibition of Rubisco activity, suggesting that mesophyll limitation was the dominant factor contributing to the decrease in C02 assimilation rates. Following re-watering, A. capensis showed remarkable recovery capacity. Fumigation of A. capensis with 1.2 ppm SO2 in the dark or light revealed relatively small effects on C02 assimilation. The inhibitory effects on photosynthesis were also fully reversible, indicating no permanent metabolic/structural damage. The effects on photosynthesis were more pronounced when fumigation occurred in the dark. This phenomenon might be related to diurnal differences in cellular capacity for SO2 detoxification. When long-term moderate water deprivation was combined with simultaneous SO2 fumigation, there was no additional inhibitory effect on photosynthesis. These findings suggest that water deprivation do not increase sensitivity towards SO2 pollution in A. capensis. Fumigation with SO2, singly or in combination with water deprivation also had no major effect on chloroplast ultrastructure. It appears that A. capensis is remarkably resistant to SO2 pollution even in the presence of low water availability, which is a common phenomenon in desert ecosystems. Since A, capensis seems to be highly tolerant to S02, its suitability as an indicator species for the detection of SO2 pollution effects at Skorpion Zinc mine is questionable. Because water availability dominates the physiological/biochemical response in this species, subtle SO2 pollution effects might be difficult to detect against this dominant background. The high water content of A. capensis and similar succulents might act as a substantial sink for SO2 and could convey considerable tolerance against this form of air pollution. / Thesis (M.Sc. (Botany))--North-West University, Potchefstroom Campus, 2006.

Methods for rapid, safe and effective detection of unmapped buried ordnance are vital to the protection of humans and environmental quality throughout the world. This study aimed to investigate the use of phytosensing and to understand the physiological response of woody plants to 2,4,6-trinitrotoluene (TNT) contamination. Baccharis halimifolia were potted in soils containing various concentrations of TNT and physiological responses were observed over a 9-week experimental period. Measurements included the collection of remotely sensed data, such as hyperspectral reflectance and chlorophyll fluorescence, and traditional plant-level physiological data. In accordance with the hypothesis, low levels of TNT improved physiological response in plants due to the slight increase in nitrogen, while high levels of TNT induced stress. Key markers in stress responses were identified, specifically with reflectance indices and derivatives, which may separate TNT-contaminated plants from naturally stressed plants and would allow for accurate detection of buried ordnance at the landscape level.

La déficience en potassium dans les parcelles de cotonnier est un phénomène répandu et en recrudescence. Le problème est d’autant plus marqué en Afrique sub-saharienne que les sols sont pauvres et les systèmes de culture peu intensifs. Les principaux effets de la carence en potassium référencés dans la littérature sont une réduction de la surface foliaire, une réduction de l’assimilation et une modification des règles de répartition des assimilats entre les compartiments de la plante (tiges, racines, fruits et feuilles). Les connaissances à l’échelle cellulaire sur le rôle du potassium sont nombreuses mais paradoxalement peu de modèles permettent l’intégration de ces résultats à l’échelle du plant et du peuplement. La raison provient de la multiplicité des mécanismes affectés et de la complexité à les intégrer à l’échelle du plant ou du peuplement. L’objectif de notre travail est de caractériser les effets de la carence en K sur la croissance et le développement du cotonnier avec suffisamment de variables intermédiaires explicatives pour pouvoir proposer un schéma conceptuel compatible avec les concepts utilisés dans les modèles de croissance de cette plante. Cet objectif implique ainsi de porter nos investigations à plusieurs échelles (peuplement, plante, organes, organites) et sur des variables-clés du fonctionnement physiologiques des plantes utilisées dans la modélisation courante telles que la photosynthèse ou le statut hydrique. Nos recherches nous ont aussi amené à mesurer d’autres variables non inclues dans les modèles courant, afin d’affiner notre compréhension du fonctionnement des plantes carencées (teneurs en sucres, vitesses de carboxylation, ouvertures stomatiques …). Pour satisfaire à ces objectifs, deux types complémentaires d’expérimentations ont été menés : 1) des essais en pleins champs, en condition pluviale strictes ont été conduits au Bénin, deux années de suite, sur deux sites différents : à Aplahoué en 2004 et à Savalou en 2005. Il s’agit d’essais comparant différents niveaux de fertilisation en potassium. L’objectif de ces essais était d’étudier les effets de la carence à l’échelle du peuplement. 2) Par la suite, une expérimentation en serre et en hydroponie a été conduite (Bordeaux, 2006) dans l’objectif d’analyser finement les processus affectés à l’échelle du plant et de l’organe. Les essais en peuplement comme l’essai en serre ont permis d’obtenir des gammes de teneur en potassium variées, grâce à des niveaux d’alimentation variés (3 niveaux au champ, 4 en serre). Les teneurs planchers des plantes les plus carencées se situaient aux alentours de 8 à 10 mg Kg-1, ce qui contraste avec les teneurs maximum mesurées qui avoisinaient les 30 mg g-1. L’indice foliaire des traitements carencés des essais en peuplement est inférieur aux témoins en raison d’un moins grand nombre de feuilles et d’une taille individuelle réduite. Dans les essais en serre, une importante réduction de la surface foliaire est aussi observée mais la part de la réduction de la surface individuelle dans la réduction de la surface totale est plus prononcée. L’analyse des dynamiques de croissance des surfaces foliaires montre que l’accroissement relatif des feuilles est identique quel que soit les niveaux de carence mais que la taille des organes à l’émergence est plus petite pour les plants carencés. En revanche, les entrenœuds des plants carencés ont à la fois une taille réduite à l’émergence et une croissance relative plus faible. A l’échelle du peuplement aucune différence d’efficience de conversion de la lumière n’est observée en conséquence, les réductions de biomasse sèche observée sont entièrement dues à une diminution de l’efficience d’interception du rayonnement. En revanche, l’efficience de conversion du rayonnement interceptée de l’essai en serre est affectée par la carence en K mais uniquement pour le traitement le plus carencé. / Potassium deficiency is a common phenomenon in cotton parcels. This problem is quite important in sub-Saharan Africa, where soils are poor and cropping systems are very low intensive. The main effects of potassium deficiency referenced in scientific literature are: (a) a reduction in leaf area, (b) a decrease in nutrient assimilation, and (c) a modification of nutrient repartition amongst compartments (i.e. stems roots, fruits, and leaves). Even though knowledge at the cellular level on the role of potassium is wide, ironically, only but a few models integrate results at the plant or stand levels. The reason comes from the multiplicity of mechanisms used and the complexity of integrating them throughout the plant or stand. The objective of our work is to characterize the effects of K-deficiency on the growth and development of cotton plants by including sufficient intermediate explanatory variables to provide a comparable scheme with the concepts used in growth models for this plant. This objective implies that our research focuses on different scales (i.e. stand, plant, organ, cell) and on physiological variables used in current models such as photosynthesis or water status. Our research had also led us to measure other variables not included in current models, to refine our understanding of the mechanisms of how deficient plants grows (i.e. sugar rates, carboxylation speed, stomata opening…). To meet these objectives, two complementary types of experiments were conducted: (i) field trials were performed in Benin on two different sites, Aplahoué in 2004 and Savalou in 2005, with strict rainfall conditions to compare different levels of potassium-fertilization and describe the effects of K-deficiency at the stand level. (ii) and a greenhouse hydroponic experiment was done in Bordeaux, France in 2006 to analyze the processes used throughout the plant and the organ. The field and the greenhouse tests had different levels of potassium fertilisation (2 to 3 levels in the field, 4 in the greenhouse) and gave us wide ranges of potassium contents in leaves. The minimum value of the leaf K content for the deficient plants were around 8 to 10 mg kg-1, which contrasts with the maximum values measured that were around 30 mg g-1. Potassium levels for the most deficient plants were around 8 to 10 mg Kg-1, while the highest levels measured were 30 g Kg-1. The leaf area index of deficient treatments is inferior to that of controls due to a lower number of leaves and smaller leaf sizes. In the greenhouse test, an important decrease of leaf area is observed but the proportion of the reduction due to a reduction in individual leaf size is more pronounced than in the filed experiments. The temporal analysis of the leaf area growth shows that the relative increase in size of the individual leaves is the same whatever the level of K-deficiency but that the size of the organs at emergence from apical buds is smaller for K-deficient plants. In counterpart, internodes of K-deficient plants have smaller lenght at emergence and a decreased relative growth rate. At stand level, no difference of light conversion efficiency is observed. As a result, observed reductions of dry biomass are essentially due to a decrease in light interception. However, radiation use efficiency in greenhouse tests are affected by K-deficiency but only for the most K-deficient treatment. Measures on gas exchanges made in greenhouse experiment also shows that photosynthesis is affected only for the most K-deficient treatments. This reduction is due to two concomitant effects: poor stomatal opening and a reduction in the maximum velocity of carboxylation. The relative distribution in biomass for all the tests is modified by the potassium-deficiency, benefiting leaves at the expense of the heterotrophic organs. This effect is observed at the plant level through an increase in the specific leaf weight and a relative decrease in stem and root biomass.

Comparés aux monocultures, les systèmes agroforestiers (SAF) sont censés permettre une meilleure efficience d'utilisation de la ressource et améliorer les services écosystémiques. Cependant, la complexité des interactions se produisant dans les SAF rend délicate la quantification et la décomposition des effets des arbres d'ombrage sur la productivité primaire nette (NPP) de la culture principale. Peu de modèles sont capables d'analyser les effets des interactions entre culture principale et arbres d'ombrage sur les échanges de CO2 et d'eau. En effet, les interactions pour la lumière, l'eau et la chaleur se produisant entre culture et arbres d'ombrage peuvent produire des effets contre-intuitifs sur la photosynthèse, l'efficience d'utilisation de la lumière (LUE), l'efficience de transpiration et le microclimat. Nous montrons que MAESPA, un modèle 3D mécaniste, peut-être utilisé pour étudier la variabilité de ces processus à des échelles allant de la plante à la parcelle, et de la demi-heure à l'année entière. MAESPA a simulé de manière satisfaisante l'interception de la lumière dans un SAF à base de caféier composé de 2 couches hétérogènes. Des variables modélisées par MAESPA ont été utilisées pour produire de puissantes variables explicatives dans un dispositif expérimental étudiant les déterminants de la NPP aérienne (ANPP) du caféier. Il a été démontré que LUE était deux fois plus élevée pour les caféiers poussant à l'ombre ce qui compensait totalement la diminution de leurs budgets lumineux, résultant en une absence de différence de ANPP entre caféiers de plein soleil et caféiers d'ombrage. MAESPA a aussi simulé de manière satisfaisante les échanges de CO2 à l'échelle du caféier et à l'échelle de la parcelle, lorsque comparés à des mesures d'échanges gazeux dans des chambres plantes entières ou à des enregistrements de flux turbulents au-dessus de la canopée, respectivement. Nous avons utilisé MAESPA pour simuler la variabilité spatiale de la photosynthèse et de LUE. MAESPA a démontré être un modèle robuste pour quantifier les interactions spatiales dans un SAF. Le prochain développement pertinent de cette approche serait de coupler MAESPA avec un modèle d'allocation du carbone dans les organes des plants de caféiers / Compared to monocultures, agroforestry systems (AFS) are expected to provide enhanced resource-use efficiency and larger ecosystem services. However, due to the complexity of the interactions occurring in AFS, it is challenging to quantify and decompose the effects of shade trees on the main crop net primary productivity (NPP). Few process-based models are able to analyze the interactions between crop and shade trees for carbon and water. Interactions for light, water and energy occurring between tree and crops might have counterintuitive effects on photosynthesis, light use efficiency (LUE), transpiration efficiency and microclimate. We showed that a 3D process-based model, MAESPA, was able to quantitatively describe the spatial variability of those processes from the plant to the plot, and from hourly to yearly timescales. MAESPA simulated satisfactorily light interception in a 2-layer heterogeneous coffee AFS. It was used to produce powerful explanatory variables in AFS experiments and to analyze the determinants of coffee plant NPP. LUE displayed a 2-fold increase for shaded coffee plants totally compensating the expected decrease of local irradiance interception, and coffee plant ANPP was the same below shade trees or in the open. MAESPA also simulated satisfactorily carbon exchange at whole plant and plot scales, when compared to gas exchange records in a whole-plant chamber, or with eddy-covariance records above the canopy. We used MAESPA to simulate the spatial variability of photosynthesis and LUE. Overall, MAESPA proved to be a relevant model to quantify spatial interactions. The next very relevant development would be to couple it to a model of carbon allocation among organs in the coffee plants

1 Abstract: The main parameters describing content and the accessibility of information from textbooks are many aspects such as text difficulty and others. Individual characteristics of pupils - that are represented by chosen student preconceptions and misconceptions - also belong to key factors. The providing of the comprehensive view of the issues regarding analysis and the linking of acquired pieces of knowledge with the practical textbook creation have been the main aims of this dissertation. The creation of an instructional text follows the analysis results of the topic carbohydrates and their metabolism in chosen textbooks and the preconception analysis of biochemical terms. The instructional text respects the results of the analysis. The theoretical background of textbook creation (the functions of textbooks, their structure, content, characteristics and investigated parameters) has been described in detail in the theoretical part of this doctoral thesis. It is followed by the survey of the information concerning student preconceptions and the possibilities for their analysis and use in teaching. The aspects of textbooks use from the perspective of pupils, teachers and publishers, as well as the relation of the topic carbohydrates and their metabolism to curriculum documents have been described in...