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Student projects

We welcome students from a variety of backgrounds to participate in our research. Our group currently has the following opportunities for carrying out a bachelors or masters research project.


1. Genome-in-a-Box: Bottom-up Reconstitution of Chromosome Organization

The molecular program of every cell is encoded in its genome. The genome size (the total number of DNA bases), varies over several orders of magnitude across organisms [1] (read more here). Despite this variety, all cells face the same critical challenge: to compact their genomes into the confined volume of a cell is a daunting task! Human cells have to compact about 1 m of DNA to 10 µm sized nucleus and bacteria about 1.4 mm of DNA to their micron sized nucleoids. How do cells do that? How do nanoscale proteins organize DNA into structures much larger then themselves? How does this influence the biophysical properties of DNA?

To contribute answers to these questions, we pursue the Genome-in-a-box project, where we isolate megabase-long DNA from live bacterium and combine it with purified proteins in microfluidic compartments which we then probe with fluorescent microscopy tools. This unique approach allows us to study the biophysics of large-scale chromosome organization, by analyzing the effects of individual DNA-organizing elements.

In context of this pursuit we have two open projects for either MEP or BEP students:

  • Characterization of size and dynamical properties of microfluidically confined chromosomes (including radius of gyration, mesh size, coefficient of diffusion, motion correlations and deformability) [2] (read more here).
  • Study of interaction of Structural Maintenance of Chromosome (SMC) proteins with isolated chromosomes [3] (read more here).

Both projects are experimental and will allow you to learn more about chromosome organization, DNA-protein interactions and microfluidics. Previous lab experience is helpful but not required. Do you find this interesting and want to learn more? Great! Please reach out to Martin Holub (m.holub[REMOVETHIS]tudelft.nl) or Alex Joesaar (a.h.joesaar[REMOVETHIS]tudelft.nl) and include a brief statement of motivation and description of your previous research experience in the email!


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2. Building and testing rationally designed nanoturbines

Flow-driven motors have powered the development of human society for thousands of years. What’s next for the era of nanotechnology?

 

Our aim in this project is to build the first-ever nanometer-sized artificial turbines using advanced DNA technologies and nanofluidics (check out our recent paper [here](https://www.nature.com/articles/s41567-022-01683-z) and [here](https://arxiv.org/abs/2206.06612)), integrate these turbines into biocompatible platforms, and use them to drive conformational changes in biomolecules. 
If you would like to join our team, you will learn/work with one of, or a combination of the following things:
  1. Basic biochemistry about handling and assembling complex DNA origami structures;
  2. Docking/inserting single nanomachines onto solid-state nanopores/lipid bilayers;
  3. Fluorescence microscopy imaging and single-particle tracking to test nanoscale turbine in action(and see your nanoturbine spinning!)


If you are interested in this project, please contact Xin at x.shi@tudelft.nl for further details.


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3. Improving our understanding of biological pattern formation

The Min protein system famously determines the cell division plane in E. coli bacteria. To this date, it remains the best-studied model system for intracellular pattern formation. However, lots of details on the inner workings of this system remain unclear. We work with reconstituted Min proteins in vitro to study their behavior, aiming to improve our understanding of biological pattern formation. New projects are currently in planning. Student (BEP) project will become available as of March 2022. International students welcome!

The work involves sample preparation, fluorescence microscopy and image analysis.

Interested? Please contact Sabrina Meindlhumer (PhD student), s.meindlhumer[REMOVE THIS]tudelft.nl for more information!


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In Figure: Min proteins forming a spiral pattern on a lipid bilayer


4. AFM-Fluorescence characterization of the plasmid partition protein ParB

A plasmid is a small, up to 2×105 pairs of bases, circular DNA molecule found inside various living organisms. The genes codified in these molecules are not essential as those codified in chromosomes, but provide some benefit for the cell (e.g. antibiotic resistance), hence, the importance of the cellular mechanisms responsible for the maintenance and organization of these molecules and their role in evolution.
 
ParB is a DNA-binding protein. The binding to DNA and polymerization of several ParB proteins could be associated with DNA condensation during cellular division, however, the specific recognition of a sequence and its utility to this mechanism remains a challenge for the scientific comunity.
 
In this project, the binding to and recognition of a specific sequence on a DNA molecule by ParB are studied using Fluorescence and Atomic-Force Microscopy. The outcome of this research project will improve our understanding of ParB’s binding mechanism to DNA.
 
For more information, contact Alejandro Martin (a.martingonzalez@tudelft.nl)
 
“Because all of biology is connected, one can often make a breakthrough with an organism that exaggerates a particular phenomenon, and later explore the generality.” – Thomas Cech, chemistry Nobel laureate 1989.

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5. Shining Light on the Nuclear Pore Complex using a Zero-Mode Waveguide

Selective transport of the Nuclear Pore Complex (NPC) can be reconstituted in minimalistic systems that consist of a solid-state nanopore functionalized with FG-nucleoporins. However, such systems present limitations in terms of biological relevance (due to applied electric field), and scalability to investigate more complex scenarios.

In this project, we tackle all these issues by with a method based on Zero-Mode waveguides (ZMW), sub-wavelength apertures in metal films (Fig.1), which we engineer with FG-nucleoporins. Even though light can not pass through the metal layer, molecules can still diffuse through the small aperture. As they reach the other side, fluorescent molecules are illuminated by the laser, one by one, resulting in single spikes in the detected signal.

With this technique we can for the first time study:
–       Selective transport at the single-molecule level in free diffusion (no applied electric field)
–       Parallel detection and discrimination of two, or more, proteins that translocate simultaneously
This approach will yield new mechanistic insights about transport through the real nuclear pore complex.

During this inter-disciplinary project you will learn how to work with ZMWs and operating a high end microscope, in order to do single molecule fluorescence experiments. Additionally, you will gather experience in
handling biological samples, functionalizing  ZMWs with purified proteins, protein labelling, and learn about the nuclear pore complex.

If this triggers you, please contact Nils Klughammer (n.klughammer@[REMOVE THIS]tudelft.nl).


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Figure 1: Zero-Mode Waveguide


6. mRNA NEXT

Compartimentalization of DNA in the nucleus is one of the central features that distinguishes eukaryotic cells from simpler organisms. Like a door connecting two rooms, a huge multiprotein complex, the nuclear pore complex (NPC), enables communication and controlled passage of molecules between the nucleus and the cytoplasm. Fundamental cellular functions, like protein production, require the messenger molecule RNA to exit the nucleus through the NPC door; yet, how this transport actually occurs is still unclear.
The final goal of the mRNA NEXT project is to recreate a minimal nuclear export system that is able to drive transport of RNA in a functional mimicking of NPC. Recreating the functionality of the NPC de novo will allow us to unravel the nature of the minimal transport complex.

We use a current-base reading that enables us to distinguish single transport events of proteins and RNA through the biomimetic NPC. Since the proteins involved perform other tasks in the cell, our unique bottom-up approach is vital to address these questions. By joining this project, you will contribute to the first-ever successful reconstruction of mRNA export in a completely in vitro system!

You will be directly involved in experimental design, trained on protein production, molecular biology techniques, single molecule nanopore technology and QCM-D, in a unique combination of interdisciplinary methods at the merge of cell biology, biochemistry and bioengineering.

We are looking for independent and enthusiast Master/Bachelor students with Physics, Biology, or interdisciplinary background. International students are especially encouraged to apply.

For more info, contact Paola De Magistris (P.Demagistris@[REMOVE THIS]tudelft.nl) or visit our labs in Applied Sciences (office 58.F0.150).


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7. The ring of power – Building a biomimetic nuclear pore complex with DNA origami

The nuclear pore complex (NPC) is a huge, ring-shaped protein system inserted into the nuclear membrane that allows only certain macromolecules to translocate into the nucleus. It is an incredibly complex system that we aim to study using a bottom-up approach.

Our goal is to build a NPC from scratch by combining different NPC proteins (nucleoporins) grafted inside a ring-like DNA origami structure. This approach gives us precise control over the stoichiometry and the positioning of individual proteins. We utilize this platform to study the arrangement and structural dynamics of the FG-nucleoporins in the pore on the single-molecule level.

By working with us, you will be directly involved in:

            •           Designing, folding and assembling DNA origami rings

            •           Protein functionalization of the DNA origami structure

            •           Analysis of the nanostructure + proteins via gel electrophoresis, mass photometry, fluorescence correlation spectroscopy

            •           Fluorescence microscopy and transmission electron microscopy

We are looking for enthusiastic Bachelor or Master students that are interested in trying to build life from the bottom up.

If you want to help us building the ring to rule them all, please contact Eva (e.bertosin@[REMOVE THIS]tudelft.nl) or Anders (a.barth@[REMOVE THIS]tudelft.nl)!


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