Speciale- og bachelorprojekter

Vi har mange forskellige projekter for Kandidat studerende og også lejlighedsvis projekter for bachelor studerende. For yderligere info kontakt Poul M. Bendix (Bendix@nbi.ku.dk) eller Liselotte Jauffred (jauffred@nbi.ku.dk).

Cellular repair system investigated by laser based nano-surgery

When cells migrate in the body they often experience membrane ruptures which results in excessive calcium flowing into the cell. This can be lethal unless the membrane is sealed within milliseconds. Cells have a built-in surface repair kit which is activated by calcium influx and hence can allow the cell to self-heal within seconds after injury. Cancer cells are extremely efficient in repairing their surface since they have an increased expression of various annexin proteins which are thought to be the major proteins involved in the membrane repair.

The project will involve testing the membrane repair system in cells by using thermoplasmonics to inflict a nanoscopic hole in the membrane. This will be done by irradiating a plasmonic gold nanostructure placed on the surface of the cell. Confocal microscopy and super-resolution microscopy will be used to monitor the recruitment of various annexins which are labeled with fluorescent proteins. The overall aims are to i) investigate whether invasive cancer cells are more efficient in dealing with thermoplasmonic ruptures than non-invasive cells ii) investigate the role of several different annexins in the repair process including other proteins like ESCRT and actin.

The project is a collaboration with Kræftens Bekæmpelse samt Syddansk Universitet.


Patterning in large bacterial communities

In nature, bacteria actively search for a surface to form larger communities, i.e., biofilm, with extended cooperativity and defense. We know that sectors with low genetic diversity form within the colony, even among cells of similar fitness. This self-organization of microbial cell communities is the result of genetic drift in complex interplay with evolution, competition, and cooperation.

We offer various projects to explore pattern formation by growing bacteria both in vivo and in silico. We believe the close interplay between theory and experiments will provide a more complete understanding of cooperation and competition among cells in larger communities.  We aim to point out general features of growth pattern, which can be generalized in wider class of systems. In the long term, we may draw parallels to mammalian cell systems, where patterning is crucial for example in embryonic development.

Possible subprojects include:

Colony shape

The relation between the individual cell shape and the colony shape

 This project combines theory and experiments depending on your interests. Experimentally, the project can include bacterial cell culture, colony growth, and advanced fluorescence microscopy. Theoretically, we plan to first simulate an individual cell-based model where the particles grow, divide, and interact through mechanical force. Depending on the development of the project, simplified lattice models or partial differential equation-based models can also be used.

Supervisors: Liselotte Jauffred & Namiko Mitarai


Investigation of the mechanism behind viral budding

Influenza virus spreads from infected cells by forming nanoscale buds on the cell surface of the infected cell. The buds emerge from nanoscale regions containing enriched densities of viral surface proteins like neuraminidase (NA) and hemagglutinin A (HA).

Clustering of viral proteins in nanoscale regions of an infected cell prior to budding.

The aim of the project is to understand which physical mechanism drives the budding of the membrane. Does the membrane bending during budding occur due to clustering of asymmetric proteins? This can be investigated quantitatively by optical manipulation of the cell surface using an optical trap in conjunction with optical tweezers. Also, the aim is to examine whether the viral proteins prefer ordered or disordered membrane phases. Nanoscale membrane phases can potentially recruit membrane proteins into small clusters and the crowding among the proteins could facilitate membrane bending and viral budding.

The project involves membrane fusion by thermoplasmonics, optical trapping, formation of giant membrane vesicles (GUVs), isolation of the plasma membrane vesicles (GPMVs) from living cells and imaging by confocal microscopy. These assays are all developed and proven feasible in our lab. This project is a collaboration with an influenza research group led by Robert Daniels at the Food and Drug Association in the States.

Contact: Poul Martin Bendix, bendix@nbi.dk


Super-resolution microscopy of subcellular structures

The living cell contains a variety of structures which fall below the standard optical resolution which is half the wavelength (~250 nm). These structures include cytoskeletal filaments, vesicles and membrane nano-domains.

Partitioning of viral membrane proteins into distinct membrane phases. Do similar phases exist at nanoscale in living cells. We can answer this by super-resolution microscopy (STORM).

We are interested in i) exploring the clustering of membrane proteins in raft like domains ii) imaging the structure of the cellular skeleton with high resolution and iii) resolve the shape of the cell surface following cell surface rupture.

The project involves using a new type of super-resolution microscope which is based on the STORM method and gives a resolution of approx. 20 nm. The biological part of the work will be carried out in close collaboration with the Nanoscience center at University of Copenhagen. Contact: Poul Martin Bendix, bendix@nbi.dk


Mechanosensing of cell

Cells have an amazing ability to sense their environment through structures on their surface. Both membrane proteins and surface nanostructures are used to sense the chemical and physical environment. This allows cells to respond to chemical and mechanical cues in the extracellular space in an appropriate manner and to convey the exterior information across the cell surface to the interior of the cell.

The cell surface is a dynamic environment with several active surface structures sensing the extracellular environment.

This project involves probing the cell surface using optical tweezers while imaging the cell response using a confocal microscopy. Several different reporters will be used based on GPCR signaling and on reporters that control the genetic transcription. The project is a collaboration with the Nanoscience Center at the University of Copenhagen. Contact: Poul Martin Bendix, bendix@nbi.dk


Brain (tumors) in a jar

Glioblastoma multiforme tumors form in brains’ white matter and remains one of the most lethal cancers, despite intensive therapy and surgery.

The poor prognosis is the result of therapeutic resistance and infiltrative growth into the surrounding brain matter. However, what triggers this infiltrative growth?

 

Possible subprojects include:

  • Cell migration from tumors.
  • Spatial regulation of epigenetic switches.

You will treat miniature brain tumors in petri dishes to measure motility, proliferation, and necrosis/apoptosis under changing conditions in the tumors’ surrounding.

This project is the result of a collaboration with the Danish Cancer Research Institute and can includes mammalian cell culture, advanced fluorescence microscopy, and image analysis.

Supervisor: Liselotte Jauffred


Spatial regulation of horizontal gene transfer

Microbes have spectacular survival capabilities and live in a wide range of environments, e.g., human guts, oceans, and soil. Microbes inherit their genomes from parental cells but can bypass this lineage via horizontal transfer of a single gene or a small group of genes. Horizontal gene transfer is considered central to the ability of bacteria to adapt to new ecological conditions.

 

Possible subprojects include:

  • Linkage of Horizontal gene transfer to fluorescence.
  • Spatial regulation of gene spreading.

The project can include bacterial cell culture, colony growth, genetics, and advanced fluorescence microscopy.

This project is the result of a collaboration with the GLOBE Institute.

Supervisor: Liselotte Jauffred


Membrane curvature shaping and sensing by proteins

Several proteins are known to induce and sense membrane curvature. This phenomenon is known to have implications in almost every curved membrane structure in the cell including endo- and exocytosis, filopodia formation, formation of intracellular membrane structures and vesicle trafficking in general.

Optical extraction of tubes from vesicles containing proteins allows investigation of curvature affinity of the protein. Annexin 5 (shown in the image) has been shown to havea  strong curvature affinity. By measuring the fluorescent intensity of the tube and the vesicle it is possible to extract the ratio between the membrane label and the protein label in two differently curved compartments.

We have developed an assay based on optical manipulation of membranes, which allows quantitative investigation of the affinity of membrane proteins for highly curved membranes. Also, we can test the ability of proteins to shape membranes by using a novel assay based on plasmonic nanoparticles.

The project involves investigation of membrane curvature sensing and induction by different proteins in both cell membranes and reconstituted membranes.

The project is a collaboration with Kræftens Bekæmpelse. Contact: Poul Martin Bendix, bendix@nbi.dk