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  • 1.
    André, Domenique
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The role of the Populus FT genes in the regulation of tree growth.2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In annual plants, flowering related genes were initially thought to have the only function to coordinate and execute reproductive development. In perennial species like poplar, however, it became clear that these genes seem to have acquired additional functions in the regulation of the yearly growth cycle. The two poplar orthologs of the Arabidopsis “florigen” FLOWERING LOCUS T (FT), PtFT1 and PtFT2, are associated with flowering as well as other aspects of phenology. After duplication they have diverged in expression pattern, and maybe also in function and their gene regulatory networks. In this study I have characterized the role of PtFT1 and PtFT2 during the yearly growth cyle, as well as the interaction between, FT-like genes, poplar homologs of the Arabidopsis flowering time repressor TFL1 and PHYTOCHROME A in the regulation of tree flowering. The preliminary data show new unexpected functional relations between these genes and new previously undescribed effects on plant growth and development.

  • 2.
    Bashar Shafiul, Shamrat
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Characterization of cell wall in transgenic aspen with modified xylan acetylation2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    ABSTRACT

    Mature plant cells are enclosed by inflexible wall made up of cellulose microfibrils, pectins, hemicelluloses and in some cases lignin. This cell wall provides the structure and the defense for plant cells. In secondary cell walls of dicotyledons, major hemicellulose is xylan consisting of β-(1, 4)-linked xylose units. Xylan is synthesized in Golgi apparatus by several enzymes activities. REDUCED WALL ACETYLATION (RWA) genes are involved in xylan acetylation. These genes were downregulated in hybrid aspen in order to reduce xylan acetylation activity during its biosynthesis. In addition, acetyl xylan esterase (FC2) from the fungus Aspergillus niger was expressed in hybrid aspen to modify xylan acetylation post-synthetically. In this work, I have studied effects of these modifications on wood cell wall composition.

    The cell wall components were sequentially extracted by using the small scale method and the weight of extractives, lignin, hemicelluloses and celluloses per weight of dry wood were determined. In addition, the Updegraff cellulose, Klason lignin contents per weight of extractive free wood were determined and monosugar compositions of non-cellulosic components were analyzed by methanolysis and Trimethylsilyl derivatisation (TMS). 

    I have found that content of cellulose determined by sequential extraction method was significantly increased in all constructs as compared to the wild type. Reduction of lignin (as determined by sequential extraction) was found in DFC2 construct and RWA RNAi 35S-AB and CD constructs. Furthermore, RWA RNAi 35S-CD and RWA RNAi WP-ABCD constructs showed decreased hemicellulose as compared to the wild type. Moreover, DFC2 constructs exhibited decrease in non-cellulosic sugars hydrolyzed during TMS. FC2 expressing lines showed a reduction in xylose which is the main building block of xylan. In contrast, glucose and galactose contents were increased. Inhibition of expression of all RWA genes (WP-ABCD) caused similar changes.

    Considering all the data I conclude that, reduced acetylation of xylan can affect extractability, biosynthesis or modification of polysaccharides and lignin in cell wall.

    Keywords: Cellulose microfibrils; pectins; hemicellulose; lignin, xylan; secondary wall; aspen; xylan biosynthesis; biosynthesis of polysaccharides. 

  • 3.
    Bañares de Dios, Guillermo
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Elucidating the role of CSK during early light response and chloroplast development2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Elucidating the role of CSK during early light response and chloroplast development

    Chloroplasts of higher plants have evolved from endosymbiotic, ancestor of modern prokaryotic cyanobacteria. During evolution most of the genes from the genome of the endosymbiont have moved to the nucleus of it host. As a consequence the components of the photosynthetic machinery are encoded both in the chloroplastic and in the nuclear genomes. Therefore, expression of both genomes must be tightly coordinated to ensure a simultaneous and stoichiometric biosynthesis of the chloroplast components at different developmental stages and under environmental or metabolic changes. This is achieved by a mechanism referred to as retrograde signalling. During retrograde signalling, signals are emitted from the chloroplast consisting on intracellular pathways emitted by the chloroplast communicating the status of the chloroplast and regulating the expression of nuclear genes encoding plastid components. The aim of this project was to elucidate the role of CSK (Chloroplast Sensor Kinase) in relation to previously described retrograde signalling components PRIN2 (Plastid Redox INsensitive 2) and GUN1 (Genomes UNcoupled 1). CSK is a plastid kinase involved in the long- term, acclimation response to balance the ratio between PSII and PSI by regulating the expression of psaA. The activity of CSK is regulated by the redox state of the plastoquinone pool. My work revealed that CSK is up- regulated upon light exposure. In addition, similarly to the prin2 and gun1 mutants, the csk mutant exhibited lower chlorophyll content, a striking yellow cotyledon tip phenotype, impaired chloroplast development and a down- regulation of PEP dependent genes psaA and psbA during a de- etiolation development and for the establishment of PEP activity in light. Furthermore, the similarity in the mutant phenotypes suggests that CSK is involved in the same signalling pathway as PRIN2 and GUN1.

  • 4.
    Brackmann, Klaus
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Contribution of endocytic trafficking and epidermal morphology genes to planar polarity formation in the Arabidopsis root epidermis2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 5.
    Claes, Andrea
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Characterization of mutants in the ACTIN-INTERACTING PROTEIN 1-2 (AIP1-2) gene of Arabidopsis thaliana and of AIP1-1 and AIP1-2 protein interactions2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 6.
    Dahrendorf, Julia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Analysis of nitrogen utilization capability during proliferation and maturation of Norway spruce (Picea abies L. Karst) somatic embryogenesis2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Around 70 % of the standing trees in northern Europe are conifers, with Norway spruce being most important. To meet future wood demands, vegetative propagation methods are offering a flexible and effective way to multiply superior genotypes. The development of nitrogen metabolism during embryogenesis is not well understood and only few studies cover conifers. Norway spruce plants prefer ammonium over nitrate as an inorganic nitrogen source. However, the proliferation of somatic embryo cultures requires organic nitrogen, and ammonium nitrate as sole nitrogen source limits somatic embryo development. This raises the question how nitrogen utilization capability advances throughout the embryo development and plant formation in Norway spruce and suggests a developmental switch in nitrogen utilization capability before the plant is fully developed. Of special interest in this context is the development and activity of three key enzymes of nitrogen metabolism: nitrate reductase (NR), glutamine synthetase (GS) and arginase.

    The aim of this study was to investigate the importance of L-glutamine as an organic nitrogen source and its impact on these key enzymes of nitrogen metabolism in the proliferation and maturation stage of Norway spruce somatic embryogenesis. Therefore media with modified nitrogen sources have been used to study the effects of presence and withdrawal of L-glutamine. Pro-embryogenic masses (PEMs) grown with L-glutamine (Gln) or L-glutamine and nitrate (Gln + NO3) showed a strongly improved proliferation rate in comparison to PEMs grown on ammonium nitrate (NH4NO3). Interestingly, GS and NR were inactive enzymatically in PEMs. Arginase activity was observed, and was unaffected by the presence or absence of L-glutamine. For analyzing the importance of L-glutamine as an organic nitrogen source during maturation, somatic embryos have been generated on media with modified nitrogen sources that included also autoclaved casein hydrolysate, an amino-acid mixture that lacks L-glutamine after autoclaving. Somatic embryos matured furthest regarding size and cotyledon development on Gln + NO3. Maturation on NH4NO3 resulted in well-developed cotyledonary stage somatic embryos that were smaller in size than in the presence of L-glutamine. In mature somatic embryos GS and NR were active. NR activity was highest, if embryos were matured on Gln + NO3 and notably lower if matured on Gln or NH4NO3. The tendentially highest GS activity was found if embryos were generated on NH4NO3. A striking change in nitrogen metabolism was the steady increase in GS activity from not detectable at proliferation stage, through easily detectable during maturation up to high activity in SE plantlets.

  • 7.
    De Bleser, Helena
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Crosstalk of ethylene and gibberellins during wood formation in hybridaspen2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Both gibberellins (GAs) and ethylene (ET) or its in planta precursor 1‐Aminocyclopropane-1‐carboxylic acid (ACC) stimulate cambial cell division and modify wood development when exogenously applied to wood forming tissues of trees. Furthermore both hormones are involved in tension wood (TW) formation in leaned trees. In Arabidopsis a cross‐talk of ET and GA on a molecular level has been demonstrated. We have examined here the effects of GA and ACC, alone and in combination, on wood development in hybrid aspen (Populus tremula x tremuloides) to investigate their potential of cross-talk during wood development. The response of selected transcripts involved in GA, ET and auxin signaling, biosynthesis and transport was inspected in the total stem of T89 trees after 10 hours of treatment with quantitative real‐time PCR (qPCR). Analysis of the phenotype, anatomy and chemistry of wild-type, ethylene-insensitive and GA‐deficient trees after 2 weeks of treatment emphasized that a cross‐talk between GA and ACC is plausible. Based on primary growth characteristics, GA and ACC seemed to be partially redundant. Lignin stainings suggest antagonistic interactions, while fiber to vessel ratios and the distribution of G‐layers put forward a collaborating action. Diffuse reflectance FT‐IR demonstrates that functional GA and ACC signalling are needed to induce differences in chemical composition.

     

  • 8.
    Decker, Daniel
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Some aspects of genetics and biochemistry of plant UDP-sugar pyrophosphorylases2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 9.
    Devadas, Arun
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Characterization of fungual strains for bioethanol production and sugar utilization2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bioethanol production from cellulose based sources is currently in focus in several research projects and the need of the hour is a versatile fermenting organism that can utilize both 5C and 6C sugars effectively. Several naturally occurring fungi have the property of fermenting both types of sugars more efficiently than the traditionally used Saccharomyces cerevisiae which only can ferment hexose sugars. In this study, six different fungi were grown on a media with sugar concentrations similar to the spent sulphite liquor (SSL) from the paper pulp industry. Known fungi such as S. cerevisiae and T. versicolor as well as 4 unidentified wood rot species were grown in sealed bottles with media containing mixture of 6C and 5C. Comparison was made between ethanol fermentation, sugar consumption and enzyme activities (ALDH and PDC). The fermentation experiment was run for 21 days and ethanol concentrations up to 18g/L were achieved. We conclude that two of the fungi produce sufficient amount of ethanol and could be used in large-scale fermentation processes.

  • 10.
    Dimotakis, Charilaos
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Understanding of the role of CAD4, CAD5 and CAD6 gene redundancy during the lignification of Arabidopsis xylem.2015Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Abstract

     

    Lignin is a cell wall polyphenolic polymer constituting the second most abundant bio-polymer on earth. This polymer is mostly accumulated in wood or xylem where it covers the other cell wall polysaccharides. Thus the removal of lignin allows accessing the polysaccharidic cell wall polymers which can then be converted into bio-fuels, textile or paper. Understanding lignin biosynthesis is therefore important to improve the industrial processing of the woody biomass. Lignin derives from the oxidative polymerization of different types of monomers called monolignols including 4-hydroxyphenylpropene alcohols as the most common monomers. Monolignols derive from the amino acid phenylalanine which is converted by a biosynthetic pathway known as the phenylpropanoid pathway. The last step of the multiple enzymatic process use the enzyme cinnamyl alcohol dehydrogenase (CAD) to convert 4-hydroxyphenylpropene aldehydes into 4-hydroxyphenylpropene alcohols. CAD is encoded by a small multigenic family in Arabidopsis thaliana comprising 17 genes.

    The aim of this master thesis is to understand the role of cinnamyl alcohol dehydrogenase gene redundancy during xylem lignification. CAD4, CAD5 and CAD6 have been associated in previous studies with xylem lignification and the main aim is to decipher if these genes are redundant or if they exhibit specificity in their expression (level, time and/or localization) and/or protein activity and structure. To do so, a genetic analysis of the single and double T-DNA insertional loss-of-function mutants in each of these genes were studied to compare their morphological characteristics, their biochemical structure (for both lignin quantification and composition) as well as their gene expression levels.

    Although minor changes in the lignin quantity and composition were observed for all of the single mutants, double mutants exhibited significant reductions and changes. Gene expression analysis moreover showed that the loss-of-function in any one of the three CADs caused a reduction ranging from 48% to 95% of the expression of the other CADs independently of the gene mutated. CAD4 and CAD5 both catalyzed the reduction of classical 4-hydroxyphenylpropene aldehydes into their corresponding alcohols: CAD5 catalytic activity is more specific to doubly methoxylated 4-hydroxyphenylpropene aldehydes than CAD4. In contrast, CAD6 did not affect the classical monolignols incorporation into lignin, but instead appeared to assist the function of CAD4 and CAD5. A clear synergetic effect of the double mutants suggested that a potential interaction could occur between these CAD proteins. Overall, our analysis showed that these three CAD genes were not redundant, but instead exhibited distinct function during xylem lignin biosynthesis.

  • 11.
    Gratz, Regina
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Expression Studies of AminoAcid Transporters belonging to the Lysine and Hisitidine Transporter (LHT) Family in Hybrid Aspen Populus tremula L. x tremuloides Michx.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The human based input of fixed nitrogen, e.g. due to nitrogenous fertilizers, is the second most important driver of global change. The active input was, however, necessary due to a fast growing demand for agricultural products in order to feed an expanding world population in the last decades. Severe environmental damages are visible now, which is why it is crucial to find alternative ways to increase plant growth and biomass production without applying massive amounts of fertilizers. One way is to identify genes, which are able to improve nitrogen use efficiency (NUE) in plants when manipulated. Especially genes involved in nitrogen uptake, assimilation and remobilization, such as amino acid transporters are of great interest. Therefore a detailed knowledge about molecular processes regarding nitrogen transport in the respective plant species is crucial. So far, there is not much known about amino acid uptake mechanisms in tree species, which is why this work focuses on hybrid aspen. It was aimed to investigate the tissue expression patterns of genes encoding putative amino acid transporters in order to find potential target genes for improving NUE in the long term.

    It was shown that eight homologs of a main Arabidopsis amino acid transporter, AtLHT1, are expressed in poplar. The eight amino acid transporters displayed different expression patterns, with expression in roots, stem and leaves of young hybrid aspen. To analyze the impacts of an increased amino acid uptake phenotype in a tree model system, PtLHT1.2 was cloned into an expression vector for Agrobacterium-mediated transformation into hybrid aspen. These results will be of great value for further studies regarding NUE in tree models.

  • 12.
    Hoengenaert, Lennart
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The role of microtubule binding proteins and post-translational modifications of tubulin during plant vessel formation in Arabidopsis2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In vascular plants, xylem tracheary elements (TEs) form the conducting tubes responsible for the hydro-mineral sap distribution between roots and leaves. Besides their role in sap transport, they also strengthen plant stems allowing upward growth of plants on land. TEs enable plants to resist mechanical constrains by laying down a thick lateral patterned secondary cell wall. The deposition of secondary cell wall material in TEs is strictly controlled by the underlying network of cortical microtubules. Such a microtubular network is a highly dynamic structure that organizes the content of the cell by anchoring or moving cellular components. The dynamic instability of the microtubules is controlled by three main factors. First, the amount of tubulin; the basic building blocks of microtubules, which are necessary for the microtubular assembly or disassembly. Second, microtubule associated proteins (MAPs), proteins capable of binding microtubules, which control microtubule stability and organization. Third, the cytoplasmic energy in GTP levels which regulate the energy dependent assembly of microtubules.

    In this research project we try to decipher if secondary cell wall patterning in TEs is achieved to a process of local microtubule stabilization or destabilization. To accomplish this, we investigated variations in tubulin quantities during TE differentiation in Arabidopsis cell cultures. Our data shows that fluctuation in tubulin levels during TE differentiation are not correlated to the process of secondary cell wall formation. In addition, we investigated how the microtubular state changes between undifferentiating and differentiating cell cultures. Using a new protocol we were able to show that differentiating TEs are enriched with stable microtubules. Since the increase in stability is not correlated to increasing tubulin amounts, other factors such as TE-specific MAPs and post-translational modifications (PTMs) of tubulin, have been investigated.

    Because such PTMs could act as molecular beacons, modifying the properties and behaviour of microtubules or its interacting MAPs, we investigated changes in tubulin-tyrosination during TE differentiation. Our experiments show a positive correlation between tubulin-tyrosination, secondary cell wall formation and the amount of available tubulin. This suggest that the tyrosination of tubulin might act as a signal for microtubular stabilization.

    Furthermore we evaluated the effect of xylem-specific MAPs on TE patterning in planta. Using tDNA mutants of MAP70-5 and MIDD1, respectively stabilizing and destabilizing MAPs, we were able to show that TE secondary cell wall patterning is mainly determined by microtubular stabilization rather than destabilization.

  • 13.
    Ilanidis, Dimitrios
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The capacity of Trametes versicolor to decompose and to produce ethanol from lignocellulose2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Lignocellulosic residues have huge potential as alternative renewable energy sources. However, lignin surrounds cellulose and hemicellulose in a complex structure that makes plant biomass highly recalcitrant to the microorganisms and enzymes that are needed for the conversion of sugars into ethanol. To extract cellulose, a diversity of pretreatments is needed. In order to evaluate the ability of the white rot fungus Trametes versicolor, a diversity of pre-treatments were analysed and the composition of the sugars released was determined. The ethanol production was measured in each case. Interestingly, pre-treatment T. versicolor resulted in a greater mono-sugar content and ethanol production in Populus spp. samples. Finally, T. versicolor was clustered with four different microorganisms in terms of genes that encode plant cell wall degrading enzymes and found to belong to the same cluster as Coprinopsis cinerea in terms of beta-xylosidase protein.

  • 14.
    Kalmbach, Lothar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Analysis of trichome polarity in the kreuz und quer (kuq) mutant of Arabidopsis thaliana and characterization of antiser against the KUQ protein2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 15.
    Kimani, Duane
    Umeå University, Faculty of Science and Technology, Department of Applied Physics and Electronics.
    Biodiesel and Hydrogen Production: A Study of Nostoc sp. in Pulp and Paper Wastewater2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The modernized world is over-consuming low-cost energy sources that strongly contributes to environmental stress. As a consequence, the interest for environmentally friendly alternatives has increased immensely. One such alternative is utilizing the diazotrophic nature of the heterocystous filamentous cyanobacteria Nostoc sp. as feedstock for biodiesel and hydrogen production using pulp and paper wastewater – a phosphorous and nitrogen deficient medium. In this work, biodiesel and hydrogen production was studied with respect to three main aspects: biodiesel quality properties, lipid content and hydrogen production coupled with a preliminary study investigating the luminous effects on the biomass and biodiesel quality properties when exposed to low (50 μEm-2s-1), medium (150 μEm-2s-1) and high light (300 μEm-2s- 1).

    The preliminary study showed that an increase of light intensity was associated with parabolic results for biomass following the 10-day cultivation period, with the medium light intensity showing an average dried weight of at the most 203% greater than the two other light intensities. When analysing the FAME- composition, similar results were demonstrated for the fatty acid constituents preferred for biofuel applications, C18:1 and C18:2 fatty acids, where the low, medium and high light showed an accumulative 34.65, 43.1 and 31.6 dwt % respectively.

    The strain could be of interest as feedstock for biodiesel when cultivated in pulp and paper wastewater, due to the positive results pertaining to the lipid content and biodiesel quality properties. Following the 10-day cultivation period the lipid content obtained was 35.9 dwt %. The biodiesel quality properties were tested to assess the strains suitability for biodiesel and were tested to ensure its accordance to the standards on commercial biodiesel quality; European Standard for Biodiesel as heating oil (EN 14213) and European Biodiesel Standard (EN 14214). The critical parameters tested were the regulated (iodine value, cetane number, density, viscosity, pour point, cold filter plugging point, oxidative stability) and unregulated (FAME-composition) fuel properties. Results obtained showed values within the regulated values set by the different standards. However, due to a high saturated fatty acid content, the strain showed inadequate low temperature flow properties (cloud point, pour point and the cold filter plugging point).

    This study shows that this strain has a low potential for hydrogen production, with a hydrogen production of 0.13 nmol/mg dry wt/h following the 10-day cultivation period. This low hydrogen production could be attributed to the among other things the current growth phase of the cyanobacteria.

    Chemical analyses were conducted for revealing the total nitrogen, total phosphorus and chemical oxygen demand (COD) content. Following the 10-day cultivation period, the samples showed a 22% decrease in phosphorous concentration, 11% decrease in COD concentration and 51% increase of nitrogen concentration. The probable causes for this increase is the Nostoc’s diazotrophic nature and the ammonium excretion nitrogen fixation entails, as well as the nitrogen release following the final algal growth phase – the death phase.

    In conclusion, the results showed great potential, however, further studies are recommended investigating the changes that occurs during cultivation period to further assess the strains potential as well as assessing the continuity of the results with a greater initial cellular concentration. Nonetheless, due to the positive results obtained regarding the nutrient uptake, biodiesel and hydrogen production, this study shows potential for further optimization for the use of Nostoc grown in pulp and paper wastewater for wastewater treatment, biodiesel and/or hydrogen production. 

  • 16.
    Lang, Patricia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    KREUZ UND QUER (KUQ) gene function during root epidermal patterning in Arabidopsis2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The patterned assignment of different cell fates, shortly termed patterning, lies at the basis of growth, development and reproduction of multicellular organisms. The single-layered epidermal tissue of Arabidopsis thaliana is characterized by hair-like cellular protuberances, the root hairs and the leaf trichomes, respectively, emerging from a subset of cells. Specification of hair and non-hair cell fate occurs in a tightly controlled fashion by gene regulatory networks of overlapping components that, however, often have opposite functions in root and shoot. Moreover, the root epidermis displays organization in hair- and non-hair cell files while leaf trichomes are distributed in a regular spacing pattern over the leaf. In contrast to the shoot, assignment of a cell file’s fate in the root epidermis depends on the cell’s position with respect to the underlying root cortical cell layer, which defines cells atop the border of two cortical cells as hair- and cells atop a single cortical cell as non-hair.

     

    The kreuz und quer (kuq-1) mutant was isolated in a genetic screen for mutations affecting cell and tissue polarity of root-hair positioning along the epidermal cell, and additional T-DNA insertion mutant alleles such as kuq-2 were identified. These mutants also display defects in cell division plane orientation in the root meristem. Preliminary observations suggested that kuq mutants may also be defective in epidermal patterning.

    In this study, light microscopic analysis revealed significant patterning defects in the root epidermis of kuq-1 and kuq-2 mutants. Both display a more random hair formation from hair and non-hair positions and an overall increased number of root hairs compared to the wild type, largely resulting from ectopic hair formation in non-hair positions. However, no hair patterning defect could be observed in the leaf epidermis of a kuq mutant. Generation and analysis of transgenic lines expressing fluorescent markers for the tubulin cytoskeleton and reporters of the non-hair fate genes WEREWOLF (WER) and GLABRA2 (GL2) in the kuq-2 mutant revealed that defects in the orientation of the cell division plane might increase non-hair-cell file duplications in the root epidermis, but did not result in the formation of ectopic hair files. To further address the effect of kuq mutation on the specification of epidermal cell fate, promoter-reporter constructs of genes with specific expression in hair- or non-hair cells were analyzed in the kuq-2 mutant. The higher incidence of fate-switches within single cell files, revealed by changes in both none-hair fate and hair differentiation markers, suggests that loss of KUQ gene function destabilizes the root epidermal pattern. To further test the involvement of KUQ in epidermal patterning and to assess possible genetic interactions, kuq-2;caprice-1 and kuq-2;wer-1 double mutants were generated and analyzed. These revealed that cpc-1 partially suppresses ectopic hair formation in the kuq-2 mutant, further supporting genetic interactions between KUQ and components of the gene regulatory network of root hair patterning.

  • 17.
    Namazkar, Shahla
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Methods to determine photorespiratory metabolic pools to improve plant productivity2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Photorespiration can limit growth of C3 plants especially under stressful conditions. Current models for future climate change predict hotter and dryer conditions in many areas, which would significantly increase photorespiration and subsequently affect crop production. Modification and engineering of photorespiration is thereby one current approach to compensate the loss of crop production affected by climate change. In this study, we employed two main strategies to better understand the dynamics of photorespiration. A counter-dogmatic accumulation of photorespiratory metabolites was identified in an Arabidopsis thaliana gox1 photorespiratory mutant therefore challenging our current understanding of the photorespiratory pathway. Here, a novel method combining protoplasts fractionation, Solid Phase Extraction and GC-MS techniques was developed to identify the sub-cellular compartmentation of these metabolites. The second strategy was detecting metabolic changes in the grass Alloteropsis semialata, which occurs as C3-, C4-, and C3-C4–intermediate (so-called C2) genotypes, using NMR-detected deuterium isotope fractionation. By exploiting the advantage that isotopomers (intramolecular isotope distributions) are a fingerprint of the regulation of photosynthetic and photorespiratory C metabolism, the deuterium isotopomer patterns of glucose derived from the genotypes allowed us to test for metabolic shifts among the genotypes. The comparison showed that there is no significant difference in isotopomer pattern among A. semialata subspecies i.e. C3, C4 and C3-C4 genotypes. These results suggest that the Calvin cycle operates with the same enzyme regulation in all genotypes. This surprising conclusion may be compatible with several previous observations, if one assumes that the C4 photosynthesis if only partly functional in the C4 genotypes. Altogether, this study contributes both technically and theoretically to better understand the dynamic of photorespiration.

  • 18.
    Norén, Louise
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Identifiction of signaling components in the response to excess light in Arabidopsis thaliana2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Even though light is essential for photosynthesis, it can also cause oxidative stress if theplant is exposed to high irradiances. Excess light results in redox changes in the chloroplastwhich can be sensed in order to mediate the information to the nucleus and adapt nucleargene expression. However, little is known about the mechanisms behind the redox sensingand light adaptive response. To investigate components involved in these pathways, twodifferent approaches were used in this study: a biochemical analysis of the transcriptionfactor bZIP16 and characterization of redox insensitive mutants isolated by a forwardgenetics approach. bZIP16 was confirmed by EMSA to interact with the G-box cis elementwhich is present in the promoters of redox/high light regulated genes, and a bZIP16:CFPfusion protein was shown to be localized to the nucleus. Characterization of the redoxinsensitive mutant rin5 revealed that these plants were unable to sense the redox changesassociated with high light exposure and adjust expression of LHCB. These results indicatethat the RI5 protein is a putative sensor of the redox changes in the chloroplast and acomponent in the signaling pathway to mediate information about light intensity to thenucleus. The bZIP16 is localized in the nucleus and binds to the G-box present in thepromoter of LHCB and possibly bZIP16 responds to the RI5 mediated plastid signal.

  • 19.
    Olofsson, Erik
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Autumn senescence in Populus tremula2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The study that was conducted in this thesis confirmed that northern aspens enter into senescence earlier and the duration of their senescence period is shorter in general compared to the more southern growing aspen ecotypes. This indicates that finishing senescence faster has a high evolutionary value the further north a tree is located. The effects of girdling and the impact it had on autumn senescence were also studied. The loss of phloem transport in girdled trees resulted in that the tree accumulated sugars that promotes the tree into a much earlier senescence and also heavily increases the anthocyanin production during the senescence initiation. These effects seem to be a response to the sugar accumulation that takes place in the tree crown as a result of the girdling. Nitrogen levels were also lower in the girdled trees but the salvage efficiency of nitrogen in the leaves increased.

  • 20.
    Potluru, Sireesha
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Phenolic profiling of Populus spp.2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 21.
    Razzak, MD. Abdur
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Physilogical changes in response to light intensity and R:FR ratio in Scots pine (Pinus Sylvestris)2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Light is crucial to plants and plants are sensitive to different aspects of light such as; light quality, quantity, duration and direction. The light signals are perceived by light receptors or photoreceptors; where phytochrome is one of the most important light receptor that perceives R and FR light and initiates the photomorphogenesis response. We studied the effect of Red (R) and Far-Red (FR) light with a range of intensities (1 µmol m-2s-1, 10 µmol m-2s-1, 25 µmol m-2s-1 and 100 µmol m-2s-1) and two R: FR ratios, 1.2 (SUN) and 0.2 (SHADOW) in Scots pine from two different latitudinal populations in Sweden (56°N and 63°N). We found that continuous R and FR light treatments significantly inhibit hypocotyl elongation and the effect was stronger with increasing light intensity. However, there was no significant effect of R light exposure on root and cotyledon growth whereas exposure to FR showed significant effect on root and cotyledon length. In addition, we observed that accumulation of chlorophyll and anthocyanin increased with increasing light intensity for both R and FR treatments. When seedlings were grown under shadow (R: FR, 0.2) longer hypocotyls were observed compared to the SUN (R: FR, 1.2) condition which is a characteristics of the shade avoidance syndrome (SAS) of the shade intolerant Scots pine. With regard to the light dominant behaviour of northern Scots pine and dark dominant behaviour of southern Scots pine (Clapham et al, 2002), ecotypic variation was observed in the the physiological responses. For instance, the pattern of development of chloroplasts differed between the two different populations from different latitudes, a significant difference of hypocotyl length following D (dark) and R light was observed between the northern and southern ecotypes. Furthermore, the southern seedlings accumulated more chlorophyll compared to the northern seedlings under SUN condition and seedlings of northern population accumulated more anthocyanin compared to seedlings of the southern population grown under both SUN and SHADOW conditions. Thus, the southern and northern populations demonstrated significant differences in many aspects of their light responses.

  • 22.
    Rende, Umut
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Role of the photosystem II-associated CAH3 in the oxygen evolving machinery in Chlamydomonas reinhardtii2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    One of the most abundant proteins on the Earth is ribulose-1,5-biphosphate carboxylase/oxygenase (RUBISCO). RUBISCO is a CO2 fixing enzyme in oxygenic photosynthetic organisms that it has low affinity for CO2. When CO2 is the limiting factor in the environment, RUBISCO works inefficiently due to its oxygenase activity. Some higher plants and aquatic photosynthetic organisms, such as the green alga Chlamydomonas reinhardtii; therefore, evolved Carbon Concentrating Mechanisms to acquire and to accumulate inorganic carbon for RUBISCO, when the CO2 concentration is at or below the air level. Carbonic anhydrases are important components of the Carbon Concentrating Mechanisms and they are zinc-containing metalloenzymes that catalyze the reversible interconversion of CO2 and HCO3−. CAH3 is one of the α-Carbonic anhydrases that it is associated with the photosystem II donor side in Chlamydomonas reinhardtii. CAH3 supplies CO2 to RUBISCO as primary function by speeding up the interconversion of CO2 and HCO3− in the thylakoid lumen. A proposed additional function of CAH3 is to regulate photosystem II by providing HCO3− to remove protons from the reaction center of photosystem II. In this report, I further test for the first time the function of CAH3 by monitoring CO2 and O2 release simultaneously from cia3 and wild type thylakoid membranes using Membrane Inlet Mass Spectrometer

  • 23.
    Sairanen, Ilkka
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Diurnaldynamics in the levels of indole-3-acetic acid in Arabidopsis thaliana2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Auxins are important regulators of growth and development in higherplants. They mediate a plethora of effects in very low concentrations viadirected movement inside and between plant tissues. These propertiesdesignate them as plant hormones. Systematic quantification of auxins havegiven important insights into its roles in various developmental processes.The levels of the main auxin, indole-3-acetic acid (IAA), have previouslybeen shown to be highly dynamic in both spatial and temporal sense. In themature leaves of Arabidopsis thaliana and Nicotiana tabacum, a daily peakof IAA, which takes place during the light period, has been established.These fluctuations have been reported to persist in continuous conditions,suggesting that an internal oscillator plays a role in the regulation, andexcluding the possibility that IAA levels would mirror the light-dependentdiurnal metabolism. Furthermore, high-throughput analysis of geneexpression imply that IAA-related metabolism include genes that are underthe control of the internal oscillator.Physiological and molecular events that show persistent patterns undercontinuous light conditions are regulated, directly or indirectly, via aninternal molecular oscillator. This mechanism, which is based on temporallyseparated reciprocal regulation of transcription factors, generates dailyrhythms that are believed to allow organisms to anticipate the transitionsbetween the light and dark periods. Successful anticipation of the transitionsis thought to bring about a significant competitive advantage.In this work, IAA levels were quantified from seelings of A. thaliana withrespect to the dark-to-light transition and to the time of day. Upon the darkto-light transition, different responses were seen between three ecotypes ofA. thaliana, proving that light-induction of IAA levels is an ecotype-specificphenomenon. Light-induction likely reflects different growth strategiesbetween the ecotypes. A time-series experiment, which followed the levelsof IAA though the day, revealed no daytime peak in A. thaliana seedlings,but did suggest a light-to-dark transition-related pulse of IAA, synthetizedin the cotyledons and flushed to the roots. Under continuous conditions, theregulation of IAA levels were found to follow the logic of hypocotylelongation: both light and an internal oscillator seemed to play a role.

  • 24.
    Siddique, Abu Bakar
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    The role of endophytic fungi in aspen leaves in the presence and absence of beetle damage2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Endophytic fungi (endophytes) are vertically (systemic) or horizontally transmitted fungi living in plant tissues without causing symptoms for at least part of their life cycle. Scientists have found evidence of a rich and diverse fungal flora in all studied plant species. The present study addressed the abundance and diversity of the endophytic community in aspen leaves and its association with aspen geno- and chemotype in the presence and absence of the leaf chewing specialist beetle Chrysomela tremulae. I found a distinct pattern of appearance and association with aspen genotypes and chemotypes when aspen leaves had no damage by beetles. This pattern changed in the presence of beetle presence and damage, endophyte richness increased and the geno- and chemotypic patterns were blurred and became insignificant. The presences of yeast-like morphs were restricted to beetle damaged plants and I could conclude that 1. Beetles may act as vectors of specific (probably yeast-like) fungi that 2. Interact with other endophytes. This insight was confirmed in a competition experiment. The fungi were identified with the use of molecular techniques using the ITS unit. Sequences were blasted against the NCBI and Yeast genome data bases. Challenges with the identification are discussed in the thesis.

  • 25.
    Sundin, Lisa
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Screening tool to unravel transcription factors involved in lignification2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Lignin is the second most abundant biopolymer and the length and complexity ofthe lignin molecule makes it a complicated molecule to study. However it playsan important role in using plant biomass for bioenergy matters since it is themajor rate limiting step. Research is now focused on engineering or lowering theamount of the molecule in planta. In this master thesis the transcription factorsinvolved in related pathways of the lignification are being studied in order todetermine transcription factors specific for the lignin pathway. This is done usinga tobacco protoplast assay system. There was at least one transcription factorthat was determined to be more lignin pathway specific. There were also someadditional findings were some transcription factors could strongly activatepromoters in pathways related to the lignin biosynthesis that had not previouslybeen described. The results described in this thesis can be an importantcontribution to the puzzle of understanding how lignin is formed.

  • 26.
    Terebieniec, Barbara
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Gene Expression and Growth Analyses in Populus RNAi lines Targeting Xylan Biosynthetic Gene Family GT 432012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Wood biomass is coming into focus as a good alternative renewable energy feedstock. Fast-growing woody plants, such as Populus species, offer potential as a bioenergy crop mediated by their abundance of energy containing cell wall polysaccharides.

    Furthermore, the first tree genome sequencing of Populus trichocarpa (poplar) offers an opportunity for genetic manipulation of woody cell components in order to optimize it for instance as an energy crop. Plant cell walls are very complex structures consisting of biopolymers, which form a network in the secondary wall. Cellulose, for instance, is organized as microfibrils consisting of β‐1,4‐glucan chains, whereas the hemicelluloses present heterogeneous polysaccharide groups. Within the hemicelluloses, xylans are the most abundant. The biosynthesis of hemicelluloses is still poorly understood.

    In order to investigate the biological role of GT43 genes during wood formation, transgenic hybrid aspen RNAi lines targeting GT43 have been created (Ratke et al., unpublished). Three GT43 genes (GT43B, GT43C and GT43F), and their double (GT43BC, GT43BF, GT43CF) and triple (GT43BCF) combinations, were selected to be targeted by RNAi. All the constructs were fused to the constitutive cauliflower 35 (CaM35S) and a wood-specific (WP) promoter and transformed into hybrid aspen (Populus tremula x tremuloides).

    The first part of the study focuses on selecting the most down‐regulated GT43 RNAi lines by using real‐time quantitative PCR analysis. We used a stepwise screening strategy starting from 20 individual in vitro transformant lines per construct. During the two in vitro screening steps we used in vitro grown stem tissue as an RNA source. The first in vitro screening narrowed down the number of lines to eight per each construct. After second in vitro screening, four most down regulated lines per construct were selected in order to grow them in greenhouse conditions and obtain woody tissue for further analyses. Third screening was applied when the GT43 RNAi plants were growing under greenhouse conditions and it used petioles as an RNA source. After the third screening, three best lines were selected per construct based on RNA analysis and additional chemical analyses not presented here. For the final gene expression analysis of selected three best lines per construct, we used freeze-dried wood or bark powder as an RNA source. The GT43 gene expression analysis base on quantitative real‐time PCR.

    These results are promising for developing Populus into a bioenergy crop. The use of molecular tools such a quantitative real-time PCR in stepwise screenings in order to select most down‐regulated lines of hybrid aspen resulted in selection of significantly altered lines as compared to the wild type. The future development of this technology should possibly use a higher number of transgenic lines as a starting point for selection.

  • 27.
    Willems, Patrick
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Receptor-like kinases regulating cold acclimation in Arabidopsis thaliana2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In temperate regions plants are able to cope with freezing temperatures after sensing lower, non-freezing temperatures through a process called cold acclimation. During the past two decades insight has been gained into the complex molecular signalling controlling the cold response. However the ‘plant thermometer(s)’ which enable plants to sense and respond to changes in their thermal environment remains to be identified. Recent studies identified a possible cold-sensor protein, mutants being unable to fully activate the ICE1-mediated CBF response pathway (unpublished results). Therefore this Arabidopsis locus was termed as cold responsive membrane kinase1 (crmk1). In phylogenetic studies crmk1 forms a discrete gene pair with crmk2, both belonging to the family of leucine-rich repeat receptor like kinases (LRR-RLKs). In this study the freezing sensitive phenotype of crmk1 was confirmed, although such effect is not observed for crmk2. Interestingly an additive effect of both genes seems present in the crmk1 x crmk2 double mutant, hinting a potential functional interplay between both LRR-RLKs. This result could not be linked to an impaired cold-induced expression of CBF genes, although future work may prove these LRR-RLKs to act as cold-sensor proteins upstream of ICE1-regulated CBF pathway.

     

  • 28.
    Xia, Hanhan
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Influence of the light harvesting proteins Lhbc3 and Lhbc5 on photosynthesis of plants lacking Lhbc1 and Lhbc2.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Photosynthesis is one of the most important biological processes on earth, producing carbohydrates and oxygen. The light is captured with the aid of light harvesting proteins. Light harvesting complex proteins in PSII are important both in light absorption and dynamic regulation. This study aims to confirm the individual role of Lhcb1 and Lhcb2 in the regulation of photosynthesis based on the KO lines: koLhcb3, koLhcb5 and koLhcb3koLhcb5. By the tool of western blot, phosphorylation analysis, state transition and non-photochemical quenching, the results indicated that the knock-out of Lhcb3, Lhcb5 or both of them did not cause additional effect on amiLhcb1 and amiLhcb2 single mutants, and then the role of Lhcb1and Lhcb2 has been complement and confirmed.

  • 29.
    Österberg, Sofia
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology.
    Transcriptional profiling of circadian clock associated genes in aspen under different photoperiods2007Independent thesis Advanced level (degree of Master (One Year)), 10 credits / 15 HE creditsStudent thesis
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