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:
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:
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:
Supervisor: Rosario Garcia-Gil, Dept of Forest Genetics and Plant Physiology, SLU.
Tel. 786 84 13. E-mail:
In col. with Universidad politénica de Valencia, Spain
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:
Background
Plants depend on their cell walls as the first line of defence when facing stress. The systems that monitor cell wall integrity (CWI) are vital, as they assess the wall’s strength and initiate responses to any damage. Key players in these responses include phytohormones, receptors, and transcription factors. In the Plant Cell Wall Dynamics group, part of our research focuses on the role of two transcription factors, ZINC FINGER OF ARABIDOPSIS THALIANA (ZAT) - ZAT11 and ZAT18. These factors are pivotal in the plant’s response to cell wall damage through their influence on phytohormone production and their interplay in regulating the cell wall integrity receptor THESEUS1 under stress conditions.
Project Overview
This project offers a molecular biology student the chance to delve into the genetic mechanisms underpinning plant resilience. By focusing on ZAT mutants and their interactions with the THESEUS1 receptor, the project aims to uncover how plants respond to cell wall damage. The use of CRISPR-Cas9 technology to generate new ZAT mutants presents a cutting-edge opportunity to advance our understanding of plant defence mechanisms.
Tasks Involved
- Crossing in Arabidopsis thaliana: You will create crosses between different ZAT mutants and the THESEUS1 receptor to study their combined effects on plant responses.
- Genotyping of Crosses: Utilising PCR, you will identify the genetic characteristics of the crosses to ensure the desired traits are present.
- Cloning into Golden Gate Vectors: This task involves cloning specific sequences into vectors for further study.
- CRISPR-Cas9 Editing: You will use CRISPR-Cas9 technology to edit the Arabidopsis thaliana genome, creating new ZAT mutants and selecting transformants.
- Cell Wall Analysis: Through techniques like monosaccharide and linkage analysis, as well as FTIR spectroscopy, you will assess the impact of mutations on cell wall composition.
- Stress Resistance Analysis: The project includes testing the mutants' resistance to various stresses such as drought, salt, and cold.
Opportunity
This project is an excellent opportunity for students interested in plant molecular biology, genetics, and biotechnology. You will gain hands-on experience in cutting-edge genetic engineering techniques, plant breeding, and biochemical analysis. This research not only advances our understanding of plant defence mechanisms but also contributes to developing crops with enhanced resilience to environmental stresses.
E-mail:
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
Background
Plant cells are encapsulated by cell walls, structures that are essential for maintaining the plant's shape, and for its interaction with environmental signals and during various growth stages. These walls play a pivotal role in development, defence, and adaptation. Cell Wall Integrity (CWI) refers to maintaining the functional and structural integrity of the plant cell wall. The CWI system adapts to environmental and growth changes by modifying the cell wall's structure and composition. With the challenges posed by climate change and the increasing demand for sustainable feedstocks, a deeper understanding of CWI is crucial. Although significant progress has been made in model organisms like Arabidopsis, there is a need to expand this knowledge by identifying more genes involved in CWI, including transcription factors and kinases, and by exploring genes in other organisms that face diverse environmental challenges.
Project Overview
This project offers a unique opportunity for a computational biology student to merge computational and experimental approaches to uncover new genes involved in CWI. By employing text mining, gene co-expression networks, and phylogenetics, this project aims to broaden our understanding of CWI across different organisms. This comprehensive approach will not only identify new candidate genes but also enhance our understanding of how plants adapt to their environment.
Tasks Involved
- Text Mining: You will sift through vast amounts of scientific literature to identify potential genes involved in CWI. This involves using software tools to scan articles for keywords related to cell wall integrity and gene functions.
- Co-expression Network: By analysing gene expression data, you will construct networks that reveal how genes involved in CWI are co-expressed under various conditions. This will help in identifying new genes that play a role in maintaining cell wall integrity.
- Finding Orthologous Genes in Other Organisms: This task involves using phylogenetic tools to identify genes similar to those known to be involved in CWI in other organisms, such as unicellular green algae. This will help in understanding how CWI mechanisms are conserved across different species.
- Functional Analysis: Through experimental biology approaches, you will validate the function of the identified genes in maintaining cell wall integrity. This might involve analysing mutants for defects in cell wall integrity or other related phenotypes.
Opportunity
This project is an exciting blend of computational and experimental biology, ideal for students passionate about plant biology, genetics, and bioinformatics. Participants will gain valuable experience in data analysis, gene network construction, and functional genomics. This research will contribute to our understanding of plant adaptation and resilience, paving the way for the development of crops better suited to changing environmental conditions.
Supervisor: Assistant Professor Laura Bacete, Dept of Plant Physiology, UMU
E-mail:
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,
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:
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:
Proteases are proteins that break down other proteins. They are involved in many different biological functions, e.g. the digestion of our food, cleaning the cell from malfunctioning proteins or cell signaling. Even though hundreds of proteases are encoded in the genomes of various plants, their biological roles are mostly unknown.
Using molecular biological and biochemical methods, we try to identify the function of a family of proteases called FtsH proteases. They are localized in mitochondria of humans, animals, plants and bacteria; in plants they can even be found in the chloroplast. While humans only have very few of these FtsH proteases, the model plant Arabidopsis thaliana contains 13 FtsH enzymes and the tree Populus has even 16 members.
Interestingly, five of the chloroplast-located FtsH homologues of A. thaliana have mutations rendering them presumably proteolytic inactive, they therefore are called pseudo-proteases. To our surprise we found one of these pseudo-proteases, FtsHi3, to be involved in drought tolerance of plants.
The research team of Prof. Christiane Funk at Umeå University and the R&D team of Dr Sacha Escamez at SweTree Technologies AB are partnering to understand how FtsHi3 could be leveraged to produce drought resistant crops. Proof of concept experiments in Arabidopsis suggested that transgenic overexpression of FtsHi3 could provide the plants with both better growth rate and improved drought tolerance, which is a very rare and very desirable combination.
This project would consist in further exploring how to optimize overexpression of FtsHi3, by using different promoters for its overexpression to become either inducible, or tissue-specific. Firstly, already transformed transgenic lines would be screened to identify the ones being homozygous for the transgene. Secondly, the expected (over)expression of the FtsHi3 gene would be tested by real-time quantitative PCR (qPCR), in regular growth conditions and during drought. Thirdly, the effect of the different overexpression strategies for FtsHi3 would be tested through drought experiments. Finally, conservation of the expected drought tolerance via FtsHi3 overexpression would be tested in Populus trees, to find if FtsHi3 overexpression could be applicable to wood crops.
Supervisor: Christiane Funk, Dept of Chemistry, UMU.
Tel. 786 76 33. 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:
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: