Exam Projects
Recent methodological advances enable the quantification of carbon fluxes across complex metabolic networks. These advances have opened an exciting new research field with a largely untapped potential. To quantify carbon fluxes, our group uses 13C Isotopically Nonstationary Metabolic Flux Analysis, a three-step procedure. In the first step, plant leaves are fed 13CO2. Assimilated 13C gradually enters all metabolite pools. In the second step, the time course of 13C enrichment of these pools is measured by mass spectrometry, a technology widely used in both academia and the industry. In the third step, leaf carbon fluxes are modelled in a software package called INCA.
In general, the master project aims at a better understanding of carbon flux through various metabolic pathways in plant leaves. Your specific research interests can be taken into account. For instance, we can try and estimate carbon fluxes in different parts of metabolism, or compare carbon fluxes among different environmental conditions, different plant species, or between mutants and wild type.
To get a better idea of the research direction, please see the following key publications:
- Ma F, Jazmin LJ, Young JD, Allen DK. 2014. Isotopically nonstationary 13C flux analysis of changes in Arabidopsis thaliana leaf metabolism due to high light acclimation. PNAS 111: 16967–16972. https://doi.org/10.1073/pnas.1319485111
- Wieloch T. 2021. The next phase in the development of 13C isotopically nonstationary metabolic flux analysis. JXB 72: 6087–6090. https://doi.org/10.1093/jxb/erab292
- Xu Y, Wieloch T, Kaste JAM, Shachar-Hill Y, Sharkey TD. 2022. Reimport of carbon from cytosolic and vacuolar sugar pools into the Calvin–Benson cycle explains photosynthesis labeling anomalies. PNAS 119: e2121531119. https://doi.org/10.1073/pnas.2121531119
Supervisor: Totte Niittylä, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 84 34. E-mail: totte.niittylä@slu.se
Co-supervisor: Thomas Wieloch, Department of Forest Genetics and Plant Physiology, SLU
E-mail:
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:
Supervisor: Christiane Funk, Dept of Chemistry, UMU.
Tel. 786 76 33. E-mail:
Plant glutamate-receptor-like channels (GLRs) function in mediating the transport of Ca²⁺ and other cations and nutrient uptakeThey are important for systemic signal propagation upon wound stress. To study their roles in roots upon wound stress, we will study the subcellular localization of 3 Arabidopsis and 5 tomato GLRs in roots. In Arabidopsis, we already have GLRpromoter::NLS-3xVenus lines and we will check the subcellular localization of GLRs in the root under normal conditions and also in the stress condition. For tomato, we will generate the tomato GLRs transgenic fluorescence marker lines (GLR promoter::NLS-3xVenus) using the root transformation method. In this study, we will do cloning, plant transformation, high- resolution imaging with microscopy, RNA isolation, qRT-PCR, and also other techniques in the areas of molecular, cell, and developmental plant biology. The project aim is to unravel the role of GLRs in roots upon wound stress
Supervisor: Peter Marhavy, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail:
The circadian clock controls a vast amount of processes in most organisms, from the cell cycle to metabolism and physiology. In this project you would characterize the function of inner clockwork in wild-type and mutant plants by tracking and analysing their leaf movements.
Supervisor: Maria Eriksson, Dept. of Plant Physiology, UMU
Tel. 090 786 51 08. Email:
The leaf epidermis consists of several cell types displaying different shapes depending on their function, including guard cells, trichomes and pavement cells. In many species, pavement cells display intriguing jigsaw puzzle-like shapes, consisting of interdigitating lobes and necks.This project will focus on the characterization of genes identified as potentially regulating lobe formation and cell shape in young pavement cells of the model plant Arabidopsis. Several of the most promising gene candidates will be cloned and tagged with fluroescent marker proteins and their localization will be characterized in detail during pavement cell lobing events. The project will combine cloning and molecular lab work with confocal microscopy techniques.
Supervisor: Stephanie Robert, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 86 09. E-mail:
This project will involve student to conduct
- Fielding measurement of growth, wood quality traits and tissue sampling for DNA and RNA extraction in Norway spruce and Scots pine
- DNA and RNA extraction and processing for genotyping and sequencing
- Genetic analyses for genome-wide association and genomic selection.
Supervisor: Harry Wu, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 82 17. E-mail:
Abstract: Among the wide variety of roots in plants, adventitious roots are post-embryonic roots developing on aerial tissues unlike lateral roots that develop on existing roots. Adventitious roots can develop as an adaptive response to various stress or as a means of propagating asexually in unfavorable conditions in nature. Most importantly, these roots are a key limiting factor during the clonal propagation of various agricultural crops including apples, berries, maize, rice and many others. Recent studies have identified various molecular regulators including phytohormones and genes that regulate adventitious rooting in Arabidopsis thaliana and other species. Although light has been suggested to participate during adventitious rooting, not much is known about this regulation (Gutierrez et al., 2009; Sorin et al., 2005). In this project, we will explore the role of light during adventitious root formation in A. thaliana using molecular biology, microscopy and genetic approaches.
Supervisor: Priyanka Mishra and Catherine Bellini, Department of Plant Physiology, UmU
Email:
Changes to intracellular metabolism confer widespread variations in epigenetic patterns and a retrograde signal may mediate chromatin modifications at regions containing photosynthesis genes. The student will be involved in a large project where we determine the distribution of important modifications of histone H3 and identify the proteins such as transcription factors or chromatin remodellers associated with those specific modifications.
Supervisor: Åsa Strand, Dept. of Plant Physiology, UMU
Tel. 090 786 93 14. Email:
Despite decades of functional genetics studies approximately 30% of the genes in the model plant Arabidopsis thaliana remain uncharacterised. In order to identify previously uncharacterized essential cell processes we investigate meristem expressed, evolutionarily-conserved single copy Arabidopsis genes of unknown function. One such gene we recently identified is OPENER (OPNR). OPNR is required for cell proliferation and localizes to both nuclear envelope and mitochondria, but the function of OPNR is still unclear. In this project, you would join the study of the OPNR and associated proteins. The project involves genetic and phenotypic analysis of mutants, quantification of gene expression and subcellular localization of proteins. You would also become familiar with the latest technologies in Crispr/Cas9-based gene editing and gene localization, 3D structure analysis of mitochondria using focused ion beam scanning electron microscope, and FLIM-FRET based protein-protein interaction.
Supervisor: Totte Niittylä, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 84 34. E-mail: totte.niittylä@slu.se
Tel. 786 86 51. E-mail:
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.
During the transition to flowering the shoot apical meristem of Arabidopsis thaliana switches fate and turns into an inflorescence meristem that gives rise to floral meristems instead of leaf primordia. As the induction of flowering is usually irreversible and to some extent determines reproductive success, plants need to make sure that this developmental phase transition occurs at the right time.
We have previously shown using ChIP-seq that the bZIP transcription factor FD binds to hundreds of loci in the genome (Collani et al., Plant Physiology, 2019). We now offer 1-2 MSc thesis projects to investigate the role of FD and the flower meristem identity gene LEAFY (LFY) in the control of flowering time and flower development using a combination of state-of-the-art molecular, genomic and genomic approaches.
Supervisor: Markus Schmid, Dept. of Plant Physiology, UMU
Tel. 090 786 58 54. Email:
Tel. 786 84 34. E-mail:
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
Tel. 786 86 51. E-mail:
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.
A Master thesis opportunity is available in the group of Alizée Malnoë (https://malnoelab.com/) in the Department of Plant Physiology at Umeå Plant Science Centre, Sweden.
The Master student will investigate the function of molecular players required for sustained energy dissipation in plants using the model organism Arabidopsis thaliana. She/he will also contribute to the characterization of suppressor 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.
Supervisor: Alizée Malnoë, Dept. of Plant Physiology, UMU
Tel. 090 786 54 59. Email:
The cuticle is a hydrophobic barrier that covers the epidermis of all land plants. This barrier is essential to plant survival and protects the plant against various biotic and abiotic stresses. The cuticle layer is also involved in regulating plant development, but the “hows” of this process remain unknown. Plants affected in cuticle composition show defects in the maintenance of several fundamental development steps that are studied in Stéphanie Robert group. In this project the student will use several techniques such as molecular biology, cell biology and biophysics to characterize the essential role of cuticle in plant development.
Supervisor: Stephanie Robert, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 86 09. E-mail:
Research themes: Our team is working on different aspects of cell adhesion in plants. We study how cells remain attached during growth and development in the model species Arabidopsis thaliana, and investigate how mechanical forces influence this process. We also study the role of the plant cytoskeleton and cell wall chemical and mechanical properties.
In parallel we also study the formation and elongation of the wood fiber cells in poplar. These cells expand by a very particular process of intrusive growth which requires a tight control of cell adhesion and is also believed to be influence by mechanical signals. This research could lead to the generation of trees with higher fiber length and wood quality.
Approaches: To study these questions we used a large range of techniques. From classical molecular biology (PCR, q-PCR, genetic constructs, CRISPR), high resolution live imaging (Confocal microscopy), image analysis, micromechanical characterization (Atomic Force Microscopy, extensometer), to computational simulations (Finite Element simulations).
Internship subject: Based on your own interest, we can discuss a range of master thesis subjects (within the research theme of the lab) that would match the type of subject that you would like to study and method that you would like to work with.
Supervisor: Stephane Verger, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 84 11. E-mail:
Plants respond to infection by changed metabolism. The attaching bacteria is counteracting these changes by affecting plant gene expression. You will be investigating this by investigating both the levels of key metabolites and expression of plant genes involved in metabolism.
Supervisor: Johannes Hanson, Dept of Plant Physiology, UmU
Tel. 786 67 44. E-mail:
Tel. 786 84 87. E-mail:
Plant nutrient uptake is a tightly controlled process. An imbalanced nutrient status affects their adaptation strategies to stress conditions and therefore impacts plant growth and productivity. A common theory is that plants rely on inorganic nitrogen (N) forms, e.g. NH4 and NO3 , as the main contributors to plant N nutrition. However, we could show that plants can also take up amino acids (AAs) to fulfill their N needs. Fine-tuning of plant nutrient management can be executed on different levels such as on protein level. It is noteworthy how little is known about the molecular underpinning of AA import regulation, in spite of that transport proteins were described already many years ago.
This project will focus on the regulation of plant nutrient transporters. You will be able to learn and apply molecular techniques such as cloning, heterologous protein expression and purification of target proteins. You will also perform Western Blot analysis in order to visualize those proteins of interest. Our PhD student will guide you through your day-to-day lab work, while you are working with us.
If you have further questions, don’t hesitate to contact us:
Contact: Torgny Näsholm,
Previously the team has developed a prototype for the study of wood quality composition in Norway spruce. The prototype will be tested in operational plantations belonging to Skogforsk (breeding center). The student will also learn to conduct genomic analysis by combining the data obtained with the prototype on wood quality and DNA information to identify genomic regions of potential value in tree breeding for wood quality.
Supervisor: Rosario Garcia-Gil, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 84 13. E-mail:
Due to its unique life cycle and relatively simple and non-redundant genome, the liverworth Marchantia polymorpha is an emerging model system for developing and testing plant synthetic biology applications. In addition, the exceptional ease with which Marchantia initiates meristems at cutting sites and regenerates into whole plants makes this species an excellent object to study the molecular mechanisms underlying regeneration. This project is focusing on the Lin28 pathway that has been previously shown to play a crucial role in the regeneration of animal systems.
In the course of the project student will acquire skills in sterile work-tissue culture techniques (vegetative propagation of Marchantia, induction of gametophyte formation and the reproductive life cycle, spore formation), molecular cloning and transformation (creating constructs for tissue-specific expression of marker genes, CRISPR/Cas9 editing, etc.), various microscopy techniques (to assess marker gene expression, immunolabeling of target proteins, etc.) as well as proteomics (to study the interactome of the Marchantia Lin28 protein).
Supervisor: Laszlo Bako, Dept of Plant Physiology, UmU
Tel.: 786 7970. E-mail:
A one year or 6 months Master’s research project position in regulation of plant energy metabolism.
The incumbent needs 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 both teaching and writing skills in English are 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.
The student will investigate how the mitochondrial metabolism contributes to pacing the nitrogen remobilization during leaf senescence in the model plant species Arabidopsis thaliana. This work will include genetics, use of knockouts and overexpressors lines, and metabolic studies on these lines.
Supervisor: Olivier Keech, Dept of Plant Physiology, UmU
Tel. 786 53 88. E-mail:
Plants maintain the potential to form new organs throughout their entire life. This capacity not only endows plants with the ability for continued growth, but also provides them with the means to adjust their growth rapidly and flexibly to changes in their environment.
We have previously shown that pre-mRNA splicing plays an important role in regulating plant growth and development in response to temperature. In particular, we could show that the SME gene PORPUCINE (PCP) is essential for normal plant development at low ambient temperature (Capovilla et al., Nature Plants, 2018).
Up to 2 MSc thesis projects are available in our group to study various aspects of how pre-mRNA splicing and long non-coding RNAs modulate temperature responses in Arabidopsis thaliana using a combination of state-of-the-art molecular, genomic and genomic approaches.
Supervisor: Markus Schmid, Dept. of Plant Physiology, UMU
Tel. 090 786 58 54. Email:
Many genetic programs are aiming at modifying crops for better processing properties of the lignocellulosic biomass in biorefinery. However, any modification of cell wall might trigger plant cell wall integrity signaling, which potentially can interfere with growth or productivity. To be able to modify crops, it is therefore essential to understand their cell wall integrity sensing pathway. We are offering a MSc project at the Umeå Plant Science Centre within the Wood Matrix Polysaccharides group of Prof. Mellerowicz investigating the secondary wall signalling pathway. The project is incorporated into a thesis work directed by the PhD student Félix Barbut.
We use the model plant Arabidopsis thaliana. The project consists of three different parts, which will be run in parallel.
In the first part of the project you will be working with transgenic plants which have defective secondary cell walls. The goal of this part of the project is to define easy-scorable phenotypes and reproducible phenotypes of these plants. These phenotypes may be include defects in seedling growth on the agar plates, altered resistance to abiotic stresses, like salt and osmotic stress, or altered morphology of soil-grown plants.
In the second part of the project, you will study different mutants selected based on previous expression network analyses and literature on cell wall integrity. We will test if any of these mutants lost the ability to react to secondary cell wall defect. The phenotypes of the mutants will be determined similar to the transgenic plants with cell wall defects. To test, our hypothesis, these mutants will be pollinated with the pollen of transgenic plants having defective secondary walls.
In the third part of the project, you will select transgenic plants in the mutant background from the progeny of pollinated plants. Such selected lines will be then compared with the lines in the WT background to confirm that the mutated genes are required for the phenotypic reaction to the altered secondary wall.
The selected student will therefore be responsible of the following studies:
- 1) Preparing agar plates and sowing seeds in vitro. The transgenic lines will then be grown for 10 days on agar plate with or without osmotic stress.
- 2) Measuring the length of the root. This is done on a high resolution photograph via the ImageJ tool which is very easy to use but it requires a certain precision. The results obtained will be tabulated in excel sheets and analysed using a statistical approach.
- 3) Following the growth of plants in a greenhouse accredited to use transgenic material. From seed to harvest, the student will be familiarized with the greenhouse safety regulations when sowing, watering, pruning plants and harvesting seeds.
- 4) Performing crosses between different transgenic plants and the mutants. This mission is essential for the continuity of the study and requires being meticulous and calm for a good success. The training will be provided.
- 5) Genotyping the generated progenies to confirm the success of the crosses using PCR.
We hope to provide a good practical educational for the student we expect the student take care to gather reliable data essential for our work. We would love to have the opportunity to discuss this project further in an interview via Zoom.
Supervisor: Ewa Mellerowitz, Félix Barbut, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail:
https://www.upsc.se/researchers/4640-ewa-mellerowicz-wood-matrix-polysaccharides-biosynthesis-and-modification.html
CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) is a recently discovered method allowing target specific genome editing in a broad range of species. It offers great hopes for the creation of point mutations or gene deletions in plant species for which genetic modification is otherwise challenging. Spruce, as a plant of large economical interest for Swedish industry, is one of them. However, setting up such a method for this perennial species represent unprecedented challenges needing to be overcome. In this project, the student will make use of the already established protocol to generate spruce protoplasts to adjust the conditions required to make CRISPR editing possible in this species.
Supervisor: Ove Nilsson, Ulrika Egertsdotter, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail:
A one year or 6 months Master’s research project position in the regulation of the protein turnover by the proteasome.
The incumbent needs 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 both teaching and writing skills in English are 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
The student will investigate how the different components of the 26S proteasome are coordinated to provide a carrefully orchestrated regulation at the protein level. Work will include genetics, molecular biology, biochemistry and physiological assays.
Supervisor: Olivier Keech, Dept of Plant Physiology, UmU
Tel. 786 53 88. E-mail:
We have investigated how TOR affect translation on a global level. The work at hand is related to testing individual genes using specific methodology in our cell culture system. Both biochemical purification of actively translating ribosome and mRNA quantification methods will be used.
Supervisor: Johannes Hanson, Dept of Plant Physiology, UmU
Tel. 786 67 44. E-mail:
We are looking for a master’s student in plant biology/molecular biology that is interested in doing a project of 10–20 weeks in Karin Ljung's group at Umeå Plant Science Centre (UPSC) in Umeå, Sweden during spring/summer 2024.
Nitrogen (N) is a principle macroelement and a growth limiting factor for plants. As sessile organisms, plants shape their root system to acquire enough N for proper growth and development. Diverse concentrations of available N as well as distinct N forms differentially affect the developmental processes of generating new lateral roots, resulting in distinct root system architecture in response to various N conditions/sources. We have shown that organic N in the form of glutamine (GLN) dramatically increases lateral root formation when compared to inorganic N treatment. In addition, lateral roots formed in response to GLN treatment are highly synchronized in their development.
This project focuses on identifying genes involved in GLN lateral root promotion by performing forward and reverse genetics screens of Arabidopsis thaliana mutant lines, using molecular biology/cloning methods coupled with confocal microscopy techniques. Moreover, highly sensitive analytical methods based on liquid chromatography – mass spectrometry (LC-MS) techniques will be used to better understand the stability, uptake and metabolism of GLN in planta.
Supervisor: Karin Ljung, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail:
https://www.upsc.se/karin_ljung
When a plant experiences stress, such as cold temperature, they upregulate a number of genes. We recently found that many of these genes have antisense non-coding transcription from the complementary DNA strand. However, the RNA produced are almost instantly degraded. The question is thus, why does the plant spend energy of producing these transcripts? One hypothesis is that the transcription itself keeps the DNA “open” so that the transcription of the genes can be boosted when the plant is exposed to stress. Another is that it modifies the chromatin environment. In order to investigate this, two types of attempts will be made to block antisense transcription; disruption of the antisense promoter by adding a T-DNA sequence, and removal of a piece of the antisense promoter using CRISPR-Cas9. We will use the model plant Arabidopsis and our goal will be to understand if non-coding transcription is required for plants to properly respond and survive stress situations.
Supervisor: Peter Kindgren, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail:
Cyst nematodes are plant parasites that induce specialized syncytial feeding structures inside the roots of their host plants. On favorable conditions, nematodes hatch from the eggs, present inside the cysts. They enter the host root from the elongation zone and migrate intracellularly to reach the vascular cylinder. During the migration phase, the nematodes cause extensive damage to the root cells. On the other hand, plants readily deposit lignin upon pathogen infection to create a physical barrier to restrict pathogen spread. In this context, MYB15 is a transcription factor that activates lignin biosynthesis genes in plant tissues under a variety of pathogen attacks. However, the role of MYB15 in plant-nematode interaction is not yet clearly understood. In a current project, we will use T-DNA knock-out mutants, MYB15 overexpression, and MYB15 marker lines of Arabidopsis plants for evaluating nematode infections. Next, the phenotypic analyses including several developed nematodes and measurements of their feeding structures will be performed. The studies will help to explore the lignification of root cells as a potential physical barrier against nematodes.
Supervisor: Peter Marhavy, Dept of Forest Genetics and Plant Physiology, SLU.
E-mail: