Exam Projects

Role of cytosine methylation in the evolution of gymnosperms genome evolution - Rosario Garcia-Gil

    Supervisor: Rosario Garcia-Gil, Dept of Forest Genetics and Plant Physiology, SLU.
    Tel. 786 84 13. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

    Characterization of FTSHi proteases of chloroplast in Arabidopsis thaliana - Christiane funk

      Proteases are highly important for cell survival. Among the large list of proteases present in plants, we are interested in the family of Filamentation temperature sensitive protein H (FtsH) enzymes, which are found in bacteria, animals and plants. Besides 12 genes encoding proteolytic active members of FtsH proteases in A. thaliana, there are 5 genes encoding for presumably proteolytically inactive proteases due to mutations in their active site; they are termed FtsHi. Despite their lack of proteolytic activity these FtsHi’s seem to be important for chloroplast and plant development, homozygous mutants of FtsHi are often embryo lethal. All five FtsHi´s are located in the chloroplast, most likely in its envelope membrane. We are elucidating the function of these presumably inactive FtsH variants. Our most recent results have been published in J. Exp. Bot. (Mishra et al., 2019).

      Supervisor: Christiane Funk, Dept of Chemistry, UMU.
      Tel. 786 76 33. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

      Identification of novel molecular players involved in plant photoprotection - Alizée Malnoë

        Identification of novel molecular players involved in plant photoprotection

        A Master thesis opportunity is available in the group of Alizée Malnoë (https://www.umu.se/en/staff/alizee-malnoe) in the Department of Plant Physiology at Umeå Plant Science Centre, Sweden.

        The Master student will identify molecular players required for sustained energy dissipation in plants using the model organism Arabidopsis thaliana. I have isolated mutants affected in photoprotection through a suppressor screen described in [1]. Using a mapping-by-sequencing strategy, the student will identify the genes mutated in mutants of interest. Whole genome sequencing will be performed at SciLife Laboratory and training for data analysis will be provided by the UPSC Bioinformatics facility. In addition, the student will contribute to the characterization of these mutants combining genetics, biochemistry, biophysics and physiology approaches.

        Please submit your letter of interest, your CV, a transcript of records of Bachelor of Science studies (if available also of the Master of Science studies carried out so far) and 1 or 2 contacts for reference to This email address is being protected from spambots. You need JavaScript enabled to view it..

        [1] Malnoë, A., Schultink, A., Shahrasbi, S., Rumeau, D., Havaux, M., and Niyogi, K.K. (2017) The Plastid Lipocalin LCNP is Required for Sustained Photoprotective Energy Dissipation in Arabidopsis. Plant Cell 30: 196-208.

        Changes of Populus root tip morphology during ectomycorrhiza formation - Judith Felten

          A Master thesis opportunity is available in the group of Dr Judith Felten at the Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences at the Umeå Plant Science Center (www.upsc.se/judith_felten), Sweden from early fall 2018 for up to 10 months.

          Project

          The Felten group is looking for a Master student, who will investigate how Populus root tip morphology changes during ectomycorrhiza formation. We have generated transgenic Populus lines expressing GFP markers localized to the nuclear envelope in a range of different root tissues. Applying a sterile culture system, the student will bring these plants into contact with ectomycorrhizal fungi and analyze marker localization and root tip morphology changes using confocal laser scanning microscopy on entire roots and root sections. Data analysis will involve image processing and analysis. In addition, the student will contribute to establishing a protocol aiming at purifying nuclei from the GFP-labelled tissues for RNA extraction and transcriptomics.

          Workplace

          Umeå is situated in the North of Sweden with easy access to Stockholm and the world. Umeå is a vibrant university town where work and leisure, cultural activities and nature are in close proximity. The Department of Forest Genetics and Plant Physiology at the Swedish University of Agricultural Sciences forms together with the Department of Plant Physiology, Umeå University the Umeå Plant Science Center (www.upsc.se), one of Europe’s strongest research centers in experimental plant biology. UPSC is a multicultural workplace employing 190 people from all over the world. UPSC’s research focuses on plant molecular biology, plant physiology, cell biology, tree biotechnology, ecophysiology and forest genetics and is supported by a large choice of specialist driven technical platforms. The student will be working in a young research group (1 PhD student, 1 technician, 4 postdocs) and will be supervised by a postdoc working in the group on a related project. UPSC has a well-developed microscopy facility that will be extended within the year 2018, which provides ideal working conditions for this project.

          Qualifications

          The student should have a background in molecular biology/plant biology and a strong interest in microscopy and image processing/analysis. Previous work with sterile culture systems as well as good computer skills are highly beneficial. The student needs to be fluent in English (written and spoken), well-organized, have good communication skills and needs to be meticulous and patient, as root manipulation, sectioning and observation are tedious tasks requiring accuracy.

          The project can be carried out for a duration of 6-10 month, where 10 months are ideal. The project will start in August/September 2018.

          Please submit your letter of interest, your CV, and at least a transcript of records of Bachelor of Science studies (if available also of the Master of science studies carried out so far) as well as 1-2 contacts for reference no later than July May 15th 2018 to This email address is being protected from spambots. You need JavaScript enabled to view it..
          Please indicate in your email subject the reference “Master_ECM2018”.

          Genetic control of energy content in Scots pine - Rosario Garcia-Gil

            Supervisors: Rosario Garcia-Gil, Dept of Forest Genetics and Plant Physiology, SLU.
            Tel. 786 84 13. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

            Molecular Regulation of Flowering, Bud Set and and Bud Break in Trees - Ove Nilsson

              Supervisor: Ove Nilsson, Dept of Forest Genetics and Plant Physiology, SLU.
              Tel. 786 84 87. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

              Field trials of transgenic aspen – Ewa Mellerowicz

                Supervisors: Marta Derba-Maceluch and Ewa Mellerowicz, Dept of Forest Genetics and Plant Physiology, SLU.
                Tel. 786 86 51. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.; This email address is being protected from spambots. You need JavaScript enabled to view it.;

                Field trials constitute the indispensable test for genetically improved trees. Transgenic aspen lines were obtained having improved growth, or wood density or with altered wood chemical traits, as determined in previous greenhouse experiments. The selected lines were planted in field trials along with wildtype plants and tested for 5-years for growth and various biotic and abiotic damages.  The trial was harvested, and the wood from this trial is being characterized. MSc project on this material is available.  The work may include various types of cell wall analyses, TGA analysis, univariate and multivariate statistical analyses, gene expression analyses.

                Characterisation of microalgae for waste water reclamation - Christiane Funk

                  For converting a society dependent on fossil fuels and nuclear energy into a sustainable, bio-based society all production processes and products must be optimized for low material and energy use. Microalgae have been shown to be a highly suitable feedstock to produce biofuels, biofertilizers or even bioplastic. In our consortium MicroBioRefine we have collected and characterized Swedish photosynthetic microorganisms such as algae and cyanobacteria for their capacity to clean waste water in our cold Nordic climate. In this project you will use biochemical and molecular biological methods to answer the following questions:
                  How can we improve the algal biomass (e.g. the lipid production)? How efficient are our Nordic microalgal strains in uptake of pharmaceuticals and other toxins? Can we improve harvesting and cell breakage by knowing more about the algal cell wall?

                  Supervisor: Christiane Funk, Dept of Chemistry, UMU.
                  Tel. 786 76 33. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                  Hemicelluloses – key determinants of wood properties - Ewa Mellerowicz

                    Supervisors: Marta Derba-Maceluch and Ewa Mellerowicz, Dept of Forest Genetics and Plant Physiology, SLU.
                    Tel. 786 86 51. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.This email address is being protected from spambots. You need JavaScript enabled to view it.

                    Hemicelluloses mediate interactions between lignin and cellulose in cell walls and thus play a key role in determining final properties of wood. We are deciphering these interactions by modifying hemicellulose structures in transgenic trees. In the project you will study effects of particular xylan modifications on tree growth and development, and on wood properties.

                    Transgenic plants will be provided. Transgene expression will be analyzed by DNA/RNA/protein activity and plants will be phenotyped by microscopy, growth analysis and various types of cell wall analyses. Possibility of field work.

                    References:

                    Pawar P M-A, Derba-Maceluch M, Chong SL, Gandla ML, Bashar SS, Sparrman T, Ahvenainen P, Hedenström M, Özparpucu M, Rüggeberge M, Serimaa R, Lawoko M, Tenkanen M, Jönsson LJ, Mellerowicz EJ*. 2017. In muro deacetylation of xylan increases lignin extractability and improves saccharification of aspen wood. Biotechnology for Biofuels, 10:98

                    Derba-Maceluch M, Awano T, Takahashi J, Lucenius J, Ratke C, Kontro I, Busse-Wicher M, Kosik O, Tanaka R, Winzéll A, Kallas Å, Lesniewska J, Berthold F, Immerzeel P, Teeri TT, Ezcurra I, Dupree P, Serimaa R, and Mellerowicz EJ*. 2015. Suppression of xylan transglycosylase PtxtXyn10A affects cellulose microfibril angle in secondary wall in aspen wood. New Phytologist 205: 666–681.

                    Characterization of inhibitors of UDP-sugar formation in plants - Leszek Kleczkowski

                      Supervisor: Leszek Kleczkowski, Dept of Plant Physiology, UMU.
                      Tel. 786 54 74. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                      Nucleotide sugars (NS) are used in hundreds of glycosylation reactions (e.g. those forming sucrose, starch, cell wall polysaccharides, such as cellulose, hemicellulose, etc.), and they represent the most important precursors for biomass production in nature. We have been studying mechanisms of formation of UDP-sugars, which are the most prominent NS, and have focused on a group of enzymes called pyrophosphorylases (namely UGPase, USPase and, to some extent, UAGPase [AGX]), which synthesize UDP-sugars from the corresponding sugar-1-phosphates,

                      Recently we have screened a chemical library, containing 18,500 compounds, for inhibitors that affect activities of purified UGPase and USPase enzymes. Seven such compounds have been identified, and they inhibited both UGPase and USPase. We also found that some of them inhibited purified UAGPase. Analogs of some of those compounds have been produced/ purchased in an effort to find even stronger inhibitors. Detailed kinetic characterization of the effects of the inhibitors and their analogs (by e.g. Dixon plots) is needed to estimate the strength and specificity of their binding to the enzymes. The work has also a drug development potential, since USPase is not present in animals, but occurs in plants and eukaryotic single-celled pathogens (e.g. Trypanosoma, Leishmania, etc.).

                      The student is expected to characterize kinetics of the inhibition by selected compounds on purified UGPase and/or USPase and/or UAGPase, using spectrophotometric approaches. The student will also apply the inhibitors to developing plant pollen to determine the in vivo effects of the inhibitors on pollen germination. For those interested in protein structure, part of the project may involve modelling of the inhibitor binding to the protein target (crystal structures for UGPase and USPase are available).

                      This can be either an exam work or 15 p project.
                      Skills required: some biochemical background, enthusiasm and critical thinking.

                      Examples of kinetic assays that can be considered:
                      •  Decker D, Lindberg S, Eriksson J, Kleczkowski LA (2014) A luminescence-based assay of UDP-sugar producing pyrophosphorylases. Analytical Methods 6: 57-61
                      •  Decker D, Meng M, Gornicka A, Hofer A, Wilczynska M, Kleczkowski LA (2012) Substrate kinetics and substrate effects on the quaternary structure of barley UDP-glucose pyrophosphorylase. Phytochemistry 79: 39-45
                      •  Meng M, Fitzek E, Gajowniczek A, Wilczynska M, Kleczkowski LA (2009) Domain-specific determinants of catalysis/ substrate binding and the oligomerization status of barley UDP-glucose pyrophosphorylase. Biochimica et Biophysica Acta 1794: 1734-1742

                       Review articles on pyrophosphorylases:
                      •  Kleczkowski LA, Decker D (2015) Sugar activation for production of nucleotide sugars as substrates for glycosyltransferases in plants. Journal of Applied Glycoscience (in press).
                      •  Kleczkowski LA, Geisler M, Fitzek E, Wilczynska M (2011) A common structural blueprint for plant UDP-sugar producing pyrophosphorylases. Biochemical Journal 439: 375-379.
                      •  Kleczkowski LA, Decker D, Wilczynska M (2011) UDP-sugar pyrophosphorylase – a new old mechanism for sugar activation. Plant Physiology 156: 3-10.
                      •  Kleczkowski LA, Kunz S, Wilczynska M (2010) Mechanisms of UDP-glucose synthesis in plants. Critical Reviews in Plant Sciences 29: 191-203.


                      From Sugar to Wood - Totte Niittylä

                        Supervisor: Totte Niittylä, Dept of Forest Genetics and Plant Physiology, SLU.
                        Tel. 786 84 34. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                        A one year or 6 months Master¹s research project position in plant cell
                        wall biosynthesis.
                        The research project is part of an effort to understand mechanisms of
                        carbon incorporation to wood cell walls with the applied goal of
                        increasing the biomass of future biorefinery feedstocks. The work is
                        carried out with Arabidopsis and hybrid aspen as model systems.
                        You need to be enrolled in a Masters degree in plant
                        biology, molecular biology, biochemistry or equivalent in a European
                        university. Knowledge in molecular biology techniques is a merit and
                        good English is a requirement. The project can be part of the UPSC
                        Masters in plant biotechnology program or be tailored to the needs of an
                        external Masters degree. For more information and to apply please send a
                        cover letter and a short CV to This email address is being protected from spambots. You need JavaScript enabled to view it.

                        The functions of the chlorophyll a/b-binding proteins - Stefan Jansson

                          Supervisors: Stefan Jansson, Dept of Plant Physiology, UMU.
                          Tel. 786 53 54. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                          How do trees know it is autumn - Stefan Jansson

                            Supervisors: Stefan Jansson, Dept of Plant Physiology, UMU.
                            Tel. 786 53 54. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                            The mediator complex organization in Poplar - a proteomic approach- Gunnar Wingsle

                              Supervisor: Gunnar Wingsle, Department of Forest Genetics and Plant Physiology, SLU
                              Tel. 786 60 61. E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

                              The Mediator complex is a part of the general transcription machinery  that’s also includes  polymerase  II in eukaryotes . It composes of  three main modules, the tail, middle and head and consists of approximately of 30 proteins all together. This complex has so far only been studied in a few articles from the plant system and this study aims to get basic information of the complex from the xylem tissue from Poplar.  The main tool will be to use masspectrometry  techniques to identify the specific components in the complex. One aim in the project will also to identify phosphorylation sites in some of the Mediator proteins.