Supervised Theses

Master theses

AuthorSchumacher, Hanna
SupervisorProf. Dr. Markus Gumbel / Prof. Dr. Lutz Strüngmann
Date2019

Abstract:

After years of research there are still many open questions on the topic of genetic code evolution. It is unclear how the code could evolve in the first place and how it could evolve as fast as it has, how its universality and ambiguity evolved and why it is not perfect in more than one aspect. Current research focuses on various aspects of genetic code evolution as for example coevolution, tRNA driven evolution, the first coding codons and coded amino acids and many more but the influence of aaRSs (aminoacyl-tRNA-synthetases) is none of the focal points.

It can be assumed that the first genetic code didn’t have the high structure of today’s code but a more random structure. A random structure means that today’s stable aaRS feedback loop hasn’t been stable in early evolution. The given aaRSs didn’t support their own reproduction but the production of other kinds of aaRSs. This behaviour is founded in an ambiguous genetic code and it is unclear how ambiguity and therefore a stable feedback cycle evolved. In this thesis it is assumed that the aaRS feedback loop was an important driver of genetic code evolution.

This thesis provides an analysis of the aaRS feedback cycle. It is applied on randomly generated genetic codes and the influence of various start conditions is observed. The process is defined mathematically and simulated with a computer simulation. The results of the simulation are analysed with the classification algorithm J48 and with sta- tistical tests to form new hypotheses that can be further explored.

AuthorBöcker, Clemens
SupervisorProf. Dr. Philipp Wiedemann
Date2018

Abstract:
In a collaboration with the Medical Faculty Mannheim of the University of Heidelberg and the KIT we work on image analysis as a means to control the quality of stored red blood cells. Recent result is a Master Thesis by Clemens Böcker, Hochschule Mannheim (2018): Flow Cytomorphometry for assessment of Red Blood Cells. In an ongoing collaboration with several internal and external partners, we work on image analysis of production process relevant animal cells (see e.g. www.imz.hs-mannheim.de/institute/research/prof-wiedemann.html). Momentarily, we focus on NS0 cells.

Bachelor theses

AuthorYuan, Mei 
SupervisorProf. Dr. Elena Fimmel
Date2019

Abstract:
Splicing is a topic that more and more people are paying attention to. The issue is particularly important because  advances in the understanding of the splicing process can lead to a breakthrough in some medical areas such as cancer research. The aim of this Bachelor thesis is to investigate whether a suitable computer model for RNA splicing can be found.  In particular, the following question is addressed: What factors influence RNA splicing and which splicing errors are caused by it?

AuthorKames, Stefanie
SupervisorProf. Dr. Lutz Strüngmann
Date2019

Abstract:
The genetic code has many facettes and one of the most ineteresting is its assignment between codons and amino acids that shows a unique redundancy. In this thesis the Fibonacci numbers will be studied and how they can be used in non-power models to describe such redunancy of ancient genetic codes and variants of the present code.

AuthorOerke, Jannik 
SupervisorProf. Dr. Markus Gumbel
PlaceThesis was done at VRmagic.
DateFebruary 2019

Abstract:

Proximity queries and penetration depth calculation of non-convex meshes is still a computationally expensive task. However this is required for real-time surgical simulations. In this thesis is selected an algorithm for calculating proximity queries as well as penetration depth for convex meshes and extended to non-convex meshes. This algorithm was implemented, integrated in a commercial collision-detection library, and examined in its real-time capability. The algorithm is based on the assumption that there exists a specific decomposition for all non-convex meshes into convex meshes at runtime. The specific requirements for this decomposition that guarantee a successful application of the algorithm are discussed and shown both intuitive and practical. This opens the possibility to construct the decomposition with moderate effort. To achieve the objective the Gilbert-Johnson-Keerthi-Algorithm for proximity queries and the Expanding-Polytope-Algorithm for penetration depths were implemented and modified accordingly. A speed analysis shows the real-time capability of the developed algorithm.

 

AuthorKarpuzoglu, Tuncay Ali
SupervisorProf. Dr. Markus Gumbel
DateMarch 2018

Abstract:

DNA contains genetic information that is passed on in every living being. It consists of a sequence of 4 bases: adenine (A), cytosine (C), guanine (G) and thymine (T). Chargaffs parity rules state that the amount of A is roughly equal to the amount of T and the amount of G is roughly equal to the amount of C even in a single DNA strand. This rule was analyzed by Mascher et al. in so called mononucleotide skews. The skew gives a concrete value for how precise Chargaffs second rule is applied in a single sequence. Petoukhov observed
further symmetries in he named tetra group symmetries.

A DNA sequence (for example, TAACCCTAACG...) can be represented in the following forms: as a text of 1-letter words (T-A-A-C-C-C-T-A-A-C-...); as a text of 2-letter words (TA-AC-CC-TA-AC-...);

The analysis of Petoukhov showed that the frequencies of every base in a 1-letter word is the same frequency as the base in each position of 2-letter words and 3-letter word, up to 5-letter words. For this thesis, five different species were analyzed, observing the skews and tetra group symmetries in those species. Another question was, whether these symmetries could be observed when comparing different parts of the DNA. To verify the significance, random models were analyzed and used as a comparative measure. Petoukhovs methods were additionally tested and applied to larger tuple sizes. The symmetries stated by Petoukhov could be confirmed for tuple sizes up to 50. When analyzing random sequences in the same manner as the chromosomes, a similar behavior was observed. These results, however, require  further biological analyses.