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Student projects


 

We warmly welcome students wishing to pursue a Bachelor or Master thesis project, as well as student projects and student assistantships. We offer a wide variety of topics and methods with a focus on the interface between theoretical and experimental biology. Find out more about current projects and join us! Open student projects are listed below, when available. If there are no offers listed, please feel free to send a research proposal.

 

 
  • Extending an existing single cell volume model for multiple cell cycles
  • Database for Cell Lines and Experiments in Cancer Research
  • Modeling the Moonlighting Fuction of Rubisco

Possible as

Studienprojekt - 3 months, Bachelor - 3 months, Projektmodul - 6 months, Master - 6 months

Contact

Björn Goldenbogen

 

 

Extending and parameterizing an existing single cell volume model to allow for multiple cell cycles.

Introduction

Single cell growth is subject to current research. Of particular interest is  the volume development of the asymmetric dividing fungus Saccharomyces cerevisae. After birth the spherical single cells expand in size and form smaller buds which separate from the mother cell after cytokinesis. Based on first principles, we already formulated a model to describe the combined growth of the mother cell and its bud. We are now searching for a student to extend the current  model to reflect the separation of both compartments and to cover multiple cell cycles, including several budding events. The model is implemented in the human readable and systems biology markup language (SBML) related modeling language Antimony (L. P. Smith et al., 2009) and simulated with the tellurium package for Python. For parameterization of the extended model a comprehensive data set of single cell volume trajectories is available.

 

Topics and Keywords

S.cerevisiae, single cell growth, mathematical modelling, Python

 

Tasks and Milestones

1.  Understand the current model

2. Integrate the termination of the first cell cycle

3. Allow for consecutive cell cycles

4. Parameterize the model  with experimental data

5. Thesis/report writing



Literature

Smith LP, Bergmann FT, Chandran D, Sauro HM. Antimony: a modular model definition language. Bioinformatics. 2009;25(18):2452-4.

Garmendia-Torres C, Tassy O, Matifas A, Molina N, Charvin G. Multiple inputs ensure yeast cell size homeostasis during cell cycle progression. Elife. 2018;7:e34025. Published 2018 Jul 4. doi:10.7554/eLife.34025

Burgert I., Fratzl P. (2006) Mechanics of the Expanding Cell Wall. In: Verbelen JP., Vissenberg K. (eds) The Expanding Cell. Plant Cell Monographs, vol 6. Springer, Berlin, Heidelberg

Tellurium Package: http://tellurium.analogmachine.org/

 

Possible as

Studienprojekt - 3 months, Bachelor - 3 months, Projektmodul - 6 months, Master - 6 months

Contact

Maria Dost

 

 

Database for Cell Lines and Experiments in Cancer Research

Introduction

Cancer research utilizes cell lines with a known mutation profile like HeLa. These cell lines are often cultivated for many generations and subjected to laboratory specific conditions and experiments and thus might show different phenotypes in quasi identical experiments. Throughout the generations these cell lines might also develop new mutations that influence the cells' behavior.


We are currently designing a database to assess the quality of published data and state of the art experiment documentation. The aim of this assessment is to improve comparability and accessibility of data.
We are looking for students to perform meta-analysis of published data on cancer cell line experiments. We want to analyze and evaluate existing data egarding the quality of the experimental data and the consistency of the results and conclusions.
The gathered data should also be added to the database and used for modeling of signaling pathways

 

 

Topics and Keywords

Cancer Cell Lines, Meta-Analysis, Signaling Pathways, Good Laboratory Practice

 

Tasks and Milestones

1. Gathering data from literature
2. Analysing data for consistency
3. Modeling of signal tranduction pathway (depends on time frame of project)
4. Thesis/Report writing

 



Literature

http://www.oecd.org/officialdocuments/publicdisplaydocumentpdf/?cote=env/mc/chem(98)17&doclanguage=en

https://reactome.org/userguide/pathway-browser

Freedman, Leonard et al. “Reproducibility: changing the policies and culture of cell line authentication”, Nature Methods, 2015

Goodman, Steven et al. “What does reproducibility mean?”, Science Translational Medicine, 2016

Kholodenko, Hancock, Kolch “Signaling ballet in space and time”, Nature Reviews, 2010

 

 

 

Possible as

Studienprojekt - 3 months, Bachelor - 3 months, Projektmodul - 6 months, Master - 6 months

Contact

Maria Dost

 

 

 

Modeling the Moonlighting Fuction of Rubisco

Introduction

The concept of moonlighting describes proteins, which perform two independent functions. Recent research has identified moonlighting proteins in a multitude of organisms. One of these proteins is Rubisco, the enzyme responsible for CO2 fixation in plants and algae. In Chlamydomonas reinhardtii, the large subunit of Rubisco seems to be able to bind RNA under certain conditions, performing a moonlighting function which helps properly assembling the Rubisco complex.

In this project, a small model of the moonlighting function of the large subunit of Rubisco should be assembled and simulated to test the effect of the moonlighting on the two pathways and their interplay.

 

Topics and Keywords

Moonlighting Proteins, Rubisco, CO2 Fixation, Chlamydomonas, ODE modeling

 

Tasks and Milestones

1. Literature research on Rubisco and its moonlighting function

2. Modeling of the two pathways, which share the moonlighting protein

3. Analysis of the effect of moonlighting

4. Thesis/Report writing

 

Literature

Cohen, Idan et al. “A conserved mechanism controls translation of rubisco large subunit in different photosynthetic organisms”. Plant Physiology, 2006

Huberts, Klei “Moonlighting protein: An intriguing mode of multitasking”, Biochimica et Biophysica Acta, 2010