Project Examples, StemPhys & Optical Tweezers
The following are master's project examples, meant to be inspirational. Inquire directly with the supervisor to find a project of interest to you and of use to the project.
Some of the projects may also be suited to bachelor projects.
Exploring the physical connection between membranes
The goal of this master’s project is to study the physical interaction between the endoplasmic reticulum (ER) and the plasma membrane (PM) and interaction which is critical for calcium uptake in cells and hence their viability. This occurs through the two membrane proteins STIM1 and ORAI1.
We are interested in how the ER-PM interaction is formed and which conditions can stimulate it. We will explore the role of STIM1/ORAI1 redistribution and complex formation under conditions of stress, such as calcium depletion of the Endoplasmic Reticulum and by extraction of the cell membrane with an optical tweezer. We are in the Optical Tweezers lab working with local heating as cancer treatment and we seek to understand molecular responses in cells exposed to localized heating. This approach will therefore tie this project to some of the overall interests of the lab.
Main Techniques: Confocal microscopy, Laser trapping of beads with Optical Tweezers, plasmonic heating, Cell cultures and transfections and membrane related techniques, cell accelerator. Data analysis using e.g. ImageJ or Matlab.
Membrane properties of lean and obese hepatocytes
In progressive obesity, excess energy is stored in organs and cells not made for lipid storage, such as muscle and liver. This accumulation of lipids presents the cells with a huge burden, which in many cases has been associated with insulin resistance and type-2-diabetes. Lipid droplet in liver cells take up physical space in the cells and comprise cellular function.
In this project, the goal is to understand the biophysical properties of liver cells, especially in the physiological condition of obesity. Thousands of cells can be analyzed in minutes to reveal physical differences between cells from lean or obese animals by using a newly developed tool called the Cell Accelerator. Additionally, single cells can be chosen for microscopic investigation of the physical environment of the cell using optical tools.
We will assess different cellular parameters and ultimately compare these observations between liver cells from lean and obese animals. This type of measurements has not yet been performed and established for liver cells, and can contain information critical for our understanding of cellular dysfunction in disease.
Main Techniques: Confocal microscopy, Laser trapping of beads with Optical Tweezers, Cell accelerator, Cell cultures and transfections and membrane related techniques. Data analysis using e.g. ImageJ or Matlab. Animal experiments will be performed at Panum.
Membrane Dynamics: Isolation of plasma membranes for studying the dynamics of proteins
Are you interested in understanding the mechanisms behind:
then you are welcome to contact me for discussing a master's project within these topics.
Main Instruments: Confocal microscopy, Micromanipulation, Optical Tweezers, Plasmonic heating of nanoparticles, Cell cultures and transfections and membrane related techniques. Data analysis using e.g. ImageJ or Matlab.
Projects will involve collaborations with: Danish Cancer Research Society Center (DCRSC) and Stockholm University
Supervisor: Poul Martin Bendix, email@example.com
Alternative insulin delivery
This project takes place mainly at Novo Nordisk, Hillerød at the Alternative Delivery department which lies in the intersection between medical device engineering and drug discovery and research. A core focus lies within alternative drug delivery technologies that can alleviate the need for frequent injections for diabetic patients. Examples of technologies in scope include oral devices, implants, and transdermal patches. Beyond drug delivery, the group explores implant devices to enable novel stem cell-based therapeutics. Concerning type 1 diabetes, a special focus is on pursuing a cure based on stem cells with the goal of developing an implantable device that can encapsulate these cells and ensure their functionality, while protecting them from the patient’s immune system.
Supervisors: Peter Herskind (Novo Nordisk) / Lene Oddershede (NBI), firstname.lastname@example.org
Analytical rheology of viscoelastic materials for insulin delivery
This project takes place mainly at Novo Nordisk, Hillerød, with the overall goal of investigating the biophysical characteristics of the polymer materials inside the Novo Nordisk pen devices. The project can be either experimental or theoretical of nature, depending on the background and interests of the candidate and may involve the following:
Methods: DMA, possibly optical tweezers, modeling.
Supervisors: Jesper Bøgelund (Novo Nordisk), Lene Oddershede (NBI), email@example.com
War of species
Spatial spreading is the most important mechanism for species to become very abundant, whether we are considering bird flocks, fungi, plants, or bacterial colonies on agar. On a surface, bacteria will align along the surface and, most often along the same axis, i.e., like rods in a box. The parallel alignment of cells is explained by cells competing for space that push against each other, and this mechanical instability leads to buckling and folding of the cell line along the surface. Hence, cell divisions in compact monolayers gives rise to topological defects as known from, e.g., liquid crystals or fingerprints.
You will investigate how different species meet and compete on a surface and, in particular, how this affects the patterning of the interface. The main aim of the project is to give a precise description of the topology of meeting fronts and the exploration of a stochastic model that includes both growth and motility. Hence, with this simple bacterial model, we can point out general features and draw parallels to mammalian cells, where migration of multicellular groups is indispensable for wound healing, embryonic development, and the infiltrative histopathology of cancer.
This project is the result of a collaboration with the University of Oxford and includes bacterial cell culture, fluorescence microscopy, and image analysis.
Supervisor: Liselotte Jauffred, firstname.lastname@example.org
Brain tumors in a jar
We offer various projects to explore possible therapeutic strategies:
You will treat miniature brain tumors in petri dishes to measure the therapeutic effect on motility, proliferation, and necrosis/apoptosis and compare to the (side) effect on normal human astrocytes.
This project is the result of a collaboration with the Danish Cancer Research Institute and can include mammalian cell culture, advanced fluorescence microscopy, and image analysis.
Supervisors: Liselotte Jauffred, Henrik Klingberg, and Lene Oddershede, email@example.com
Patterning in large cell communities
We have most of our knowledge about microbes from liquid cultures, where bacteria
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:
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, firstname.lastname@example.org