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Master’s degree project in molecular biology

Interested in carrying out a degree project? If you don't find any of the projects below to your liking, please contact any of the research groups at our department.

Proposals in:

Animal physiology

Master degree projects in the cell proliferation group

In our research group we are investigating molecular mechanisms regulating cell proliferation and apoptosis in normal cells and cancer cells. We are performing basic research as well as applied research with the goal to aid in better chemotherapeutic treatment of cancer patients. We are also investing how various food components are affecting cell proliferation and apoptosis. This may have implications for cancer development and progression. Potential master degree students must have attended courses with a fair amount of cell culturing in practicals or have worked with cell culturing in other settings. In exceptional cases we can accept master students in projects that do not include cell culturing but only other methods used in the lab (Western blot, fluorescence microscopy, enzyme analysis etc).

Below you will find examples of projects:

Effect of chemotherapeutic treatment on cancer stem cells in neuroblstoma grown in normoxia or hypoxia

Neuroblastoma cells grown in culture under normoxic and hypoxic conditions will be treated with chemotherapeutic drugs. The effect under different cellular populations will be investigated using flow cytometry and immunofluorescence microscopy after labelling with different antibodies.

Effect of chemotherapeutic treatment on cancer stem cells in breast cancer grown in normoxia or hypoxia

Breast cancer cells grown in culture under normoxic and hypoxic conditions will be treated with chemotherapeutic drugs. The effect under different cellular populations will be investigated using flow cytometry and immunofluorescence microscopy after labelling with different antibodies.

Dose response studies of combining chemotherapeutic drugs on cells cultivated in normoxia or hypoxia

We have various molecularly based hypothesis of how to combine new chemotherapeutic drugs. These have to initially be tested in 96-well dose response assays to get information of proper combinations, treatment times and concentrations. The next step is to investigate if our molecular hypotheses are true. To this end, the expression of different proteins will be investigated by Western blot.

Please contact Stina Oredsson if you are interested in these proposals.

Genetics

Saccharomyces castellii: a new yeast model system

The protein counting model for telomere length regulation
The RAP1 proteins bind to the telomeric DNA. When a threshold number is reached, further telomere elongation by telomerase is inhibited.

The yeast species Saccharomyces castellii has regular 8 bp telomeric repeats and a telomerase activity similar to that of human cells. In this advantageous species we want to analyze the effect on telomeres when various telomere related genes are mutated. By measuring the length of telomeres we will be able to get information on whether the specific genes are involved in a positive or a negative regulation of telomere length.

The project will involve many molecular biology methods such as cloning, PCR, DNA sequencing, computational sequence analyses, transformation, DNA extractions, and Southern blot hybridizations. Moreover, the RNA interference (RNAi) pathway has been identified in this species and can be used as a tool to knock down the expression of specific genes.

Please contact Marita Cohn if you are interested in this proposal.

How does Cdc13 regulate the telomerase elongation?

Protective cap on the chromosome

The telomeric DNA sequences are bound by a number of different proteins which build up a protective cap on the chromosome. The RAP1 protein and its interacting partners Rif1 and Rif2 have been shown to regulate the length of the telomere, probably by controlling the access of telomerase to the end of the chromosome.

The protein Cdc13 binds to the single-stranded overhangs at the very ends of telomeres. In Saccharomyces cerevisiae the Cdc13 was determined to be essential for the recruitment of telomerase to the telomere end. However, Cdc13 may also act as an inhibitor of telomerase by interacting with Stn1 and Ten1 (the CST complex). We have found that the Cdc13 homolog in Saccharomyces castellii (scasCdc13) has very interesting DNA-binding features. The minimal binding site of eight nucleotides contains a GT-GG motif which is conserved among various different species, including human cells. Now we would like to know more about why and how this protein binds to this specific sequence at the ends of chromosomes and how it functions as a regulator of telomerase.

The project will involve molecular biology methods such as cloning, PCR, transformation, expression of recombinant protein, and protein affinity purification. The DNA binding will be measured by the Electrophoretic Mobility Shift Assay (EMSA) and the possibility for the telomerase to extend the telomere is analyzed by telomerase activity assays.

Please contact Marita Cohn if you are interested in this proposal.

Microbiology

Molecular basis of heme and hemoprotein biogenesis

Heme, a closed ring tetrapyrrole with an iron atom ligated in the center, is an essential cofactor for most cells. It is the prosthetic group of important proteins such as hemoglobins, cytochromes, and catalase. We have considerable knowledge about the structure and function of hemoproteins but little is known about how such proteins are assembled in cells and how specialized heme variants, e.g. heme A and D, are synthesized. Using bacteria, mainly Bacillus subtilis, Escherichia coli and Entercoccus faecalis, as experimental systems we study heme synthesis and assembly of hemoproteins.

Publication: Hederstedt, L. Heme A biosynthesis. (2012). Biochem Biophys Acta. 1817: 920-927. Baureder M., Barane E. and L. Hederstedt. In vitro assembly of catalase. (2014) J Biol Chem 289: 28411-28420.

Please contact Lars Hederstedt if you are interested in this proposal.

Endospore biogenesis

Bacterial endospores, mainly of the genera Bacillus and Clostridium, are the hardiest forms of life known. They withstand treatment with heat and chemicals that otherwise kills cells. The cortex layer of the endospore mainly consists of a modified type of peptidoglycan and is essential for heat-resistance. A penicillin-binding protein, SpoVD, plays an essential role in cortex synthesis. The project aims to elucidate the functions of SpoVD at the molecular level.

Publication: Bukowska-Faniband, E. and L. Hederstedt. Cortex synthesis during Bacillus subtilis sporulation depends on the transpeptidase activity of SpoVD. (2013) FEMS Microbiol Lett. 346: 65 -72. Bukowska-Faniband, E. and L. Hederstedt. The PASTA domain of penicillin-binding protein SpoVD is dispensible for endospore cortex peptidoglycan assembly in Bacillus subtilis. (2015). Microbiology 161: 330-340..

Please contact Lars Hederstedt if you are interested in this proposal.

Biology of a bacterial redox sensing system

Bacteria use various signal-transduction systems to sense and respond to their environments and survive in a range of biological niches. Coping with a new environment requires both increasing expression of some genes and turning off the expression of others. In this project you will study how bacteria adapt to redox stress caused by an excess of reduced nicotinamide adenine dinucleotide (NADH) in the cytoplasm. During aerobic growth the reducing potential stored in NADH is converted to ATP via the electron transport chain or used for anabolic metabolism. Reductive stress occurs when NADH is not reoxidized to NAD+ as a result of for example inefficient respiration. In gram-positive bacteria a conserved transcriptional regulator called Rex is present. It controls the expression of genes involved in respiration and fermentation in response to changes in the intracellular concentration of NADH. In this project you will use a combined molecular genetic and biochemical approach to investigate structural and functional properties of the Rex transcriptional regulator. You will get hands-on experience with DNA manipulation, structural bioinformatics, recombinant protein production and analysis.

Further reading:

  • Green, J., and M. S. Paget. 2004. Bacterial redox sensors. Nat Rev Microbiol 2:954-966.
  • Wang, E., M. C. Bauer, A. Rogstam, S. Linse, D. T. Logan, and C. von Wachenfeldt. 2008. Structure and functional properties of the Bacillus subtilis transcriptional repressor Rex. Mol Microbiol 69:466-478.

Please contact Claes von Wachenfeldt if you are interested in this proposal.

How are bacteria coping with stress?

Just like us, bacteria have to deal with stress all the time. However, stress for bacteria is a bit different from the stress we are used to – it is something that causes damage to the cellular macromolecules: membranes, proteins and nucleic acids. It can be chemical stress, caused by harmful compounds, or physical stress, for example heat. Bacteria have developed stress responses, which aim to temporarily increase tolerance limits. These stress responses are often very specific; each specialized in a particular kind of stress. Some stress responses facilitate bacterial transition from a free-living organism to a host-invading pathogen. In this project you will investigate how the soil-living bacterium Bacillus subtilis or the opportunistic pathogen Staphylococcus aureus deals with oxidative stress and other types of stress that leads to protein aggregation. We use a combined genetic and biochemical approach to study bacterial stress responses. Depending on the particular aspects of stress management you chose to study you will get hands-on experience with a number of methods that may include; cultivation of bacteria, DNA manipulation, live cell imaging, immunofluorescence microscopy, protein production, characterization and crystallization.

Further reading:

  • Zuber, P. 2009. Management of oxidative stress in Bacillus. Annu Rev Microbiol 63:575-597.
  • Engman J., von Wachenfeldt C. 2015. Regulated protein aggregation: a mechanism to control the activity of the ClpXP adaptor protein YjbH. Mol Microbiol 95: 51-63.

Please contact Claes von Wachenfeldt if you are interested in this proposal.

Molecular plant biology

Recommended project length is 45-60 points. Projects can be designed with concern to student background and orientation (e.g. plant physiology, biotechnology biochemistry or molecular biology).

NAD(P)H redox regulation in plants

The soluble redox carriers NAD(H) and NADP(H) are central mediators of reductant between metabolic processes, energy transduction and stress response components.

a) In transgenic plants modified with respect to mitochondrial pathways of NADH and NADPH oxidation (Type II NAD(P)H dehydrogenases), it is possible to directly asses the importance of the cellular pools of these reductants for involvement in tolerance to particular biotic and abiotic stresses.

b) In isolated mitochondria and after expression in E. coli, the regulatory properties of NAD(P)H dehydrogenases are studied biochemically.

Articel at Biochemical Society Transactions with background info on NADP(H) redox regulation.

Please contact Allan Rasmusson if you are interested in this proposal.

Interactions between plants and fungal peptides

Benevolent fungi protect plants and are therefore used for biocontrol of pathogens. In particular, Trichoderma fungi kill bacteria and other fungi by excreting antimicrobial peptides. Plants protect themelves against these peptides by inducing unknown molecular changes to their cellular functions. Degree projects can be designed aiming at discovering components and mechanisms involved in how the plant resistance is elicited and signaled and how plant cell components are modified in order to become protected.

Please contact Allan Rasmusson or Susanne Widell if you are interested in this proposal.

External projects related to cell and molecular biology

>Cell extravasation in microfluidic vascular models

Today, a highly artificial in vitro tissue culture system is used to study cancer and leukocyte function. Instead, we plan to use of “lab on a chip”, which is a more physiologically relevant model and therefore a better replacement for today studies using animals. Our aim with this project is therefore to development of more relevant and advanced human physiological model, which will increase the number of researchers, who will choose to go from animal models to human in vitro models. This will not only lead to reduced use of unnecessary animals in the academic and pharmacology industry research community but also lead to refined experiments control, giving the user control over several parameters not possible in an in vivo setting. Our aim with this project is to adopt in vitro microfluidic vascular models and use these to study cancer metastasis and leukocyte transmigration.

Cancer metastasis is the process during which cancer cells leave their original tumour, move through the surrounding tissue and enter the vascular system. The cancer cells travel through the vascular system and eventually cross the vessel walls (extravasation) and establish new tumours, with detrimental consequences to the patients. The mechanisms involved in this process are poorly understood and current knowledge relies heavily on animal experiments, either as an end point assay or as highly invasive intravital microscopy. Cancer metastasis is today the biggest cause of fatal ending of the disease and 80% of death is caused by metastasis, and it is therefore of great importance to be able to prevent uncontrolled migration of tumour cells. Student project: The proposed project student will learn to culture endothelial cells in channels, covering an extra cellular matrix (ECM) model, creating a model interior vessel wall. Further study in high resolution, mechanistic studies of cell migration and other cell functions by using advanced microscopy.

Please contact Lena M Svensson, Leukocyte Migration Lab

Mycobacterial suppression of adaptive immunity – implications for vaccine development

Mycobacteria, and particularly Mycobacterium tuberculosis (Mtb), represent a major threat to human health globally. About one third of the world’s population is infected with Mtb, a human pathogen responsible for ~2 million deaths annually. The health problem posed by Mtb is worsened by poor efficacy of current vaccine regimens and by emergence of multi-drug resistant strains, threatening to undermine both disease-prevention and current treatments. Indeed, the only licensed vaccine against tuberculosis (Bacillus Calmette-Guerin [BCG]) shows an overall protection of merely 25-50%. Moreover, these numbers primarily reflect protection against severe disseminated forms of tuberculosis in children, and the vaccine does not similarly protect against lung disease nor does it provide sterile immunity. It is well established that Mtb is able to prevent the establishment of adaptive immunity for three weeks. When compared to other intracellular pathogens, such as Legionella Salmonella or Influenza, this delay is astonishing and suggests that mycobacteria have evolved effective strategies to suppress the adaptive immune response. While these strategies likely are central to the chronic character of tuberculosis and to the poor efficacy of the BCG vaccine (since they will allow mycobacteria to go “under the immunological radar”), the responsible host-pathogen interactions have remained unknown.

To address this key problem and to generally facilitate fundamental studies into Mtb pathogenesis, we use the safer and experimentally more amenable Mycobacterium marinum (Mmar), which is closely related to Mtb, as a model system. Preliminary results from a mouse model of Mmar infection suggest that we have identified both mycobacterial and host genes required for mycobacterial suppression of adaptive immunity. Based on these initial findings our current studies are aimed at providing a molecular explanation to how mycobacteria impede specific immunity. Such knowledge will represents a major step forward in our understanding of mycobacterial pathogenesis, and will likely impact vaccine design as well as suggest novel avenues for immunotherapy of tuberculosis.

Please contact Fredric Carlsson if you are interested in this proposal.

New targets to study chronic pain

Chronic pain is a public health problem in need of new and improved treatment options. It is often difficult to diagnose the cause of chronic pain and neuroscientists often say "the rain of pain falls mainly in the brain", that is, the cause is likely due to changes in the central nervous system.

The Master project involves the study of a hitherto somewhat neglected structure in the inner parts of the brain that we believe is a key to understanding the neural changes that occur during the development of chronic pain. We have developed technology that allows us to measure and monitor the activity in individual brain areas for a long time. This provides new knowledge about how painful information is processed in the brain. An important element of the project is to examine in detail the signal pathways from our target areas. By tagging a specific group of neurons, we can find out which brain areas these cells contact.

We are now looking for someone with a thorough interest in brain research, that has experience in histology, sectioning of tissue and microscopy. Basic neuroscience skills and experience of animal handling is a prerequisite. The project is demanding and will require independent work, but can provide unique new understanding of the brain and the mechanisms behind chronic pain. If this sounds interesting, don’t hesitate to contact us and we'll talk more!

Please contact Marcus Granmo if you are interested in this proposal.

Page Manager:

Study advisor

Christina Ledje, Education Office
Christina.Ledje [at] biol.lu.se
046-222 73 16

Administrator

Jóhanna B. Jónsdóttir, Education Office
Johanna_B.Jonsdottir [at] biol.lu.se
046-222 73 15

Coordinators

Main coordinator

Klas Flärdh, room B-A222a
Klas.Flardh [at] biol.lu.se
046-222 85 84

Specialization in Medical Biology

Bodil Sjögreen, room B-B205
Bodil.Sjogreen [at] biol.lu.se
046-222 93 48

Specialization Molecular Genetics and Biotechnology

Marita Cohn, room B-A107A
Marita.Cohn [at] biol.lu.se
046-222 72 56

Specialization in Microbiology

Lars Hederstedt, room B-A242
lars.hederstedt [at] biol.lu.se
046-222 86 22

One-year Master's (Magister)

Torbjörn Säll, room B-A334
Torbjorn.Sall [at] biol.lu.se
046-222 78 58