Decoding worms to decode regeneration

Dr. Siegfried Schloissnig is head of the newly established Computational Biology junior research group at Heidelberg Institute for Theoretical Studies (HITS). Prof. Eugene “Gene” Myers, one of the pioneers in bioinformatics, is affiliated with the group as a mentor. Together with his laboratory at the Max Planck Center for Systems Biology in Dresden, the junior group will decipher and compare the genetic codes of several flatworm species. Flatworms are masters of regeneration, and are, therefore, interesting for scientists: If they are cut in two pieces, each half will develop into a new worm. By comparing the genetic material, researchers hope to  gain new insights into regeneration of tissue that could have a huge impact on medicine.

A new junior research group for Computational Biology (CBI) has been established at Heidelberg Institute for Theoretical Studies (HITS). It complements the work of the other six research groups, which carry out basic research in different fields of science. The focus lies on the processing and structuring of large data volumes. The leader of the new group is Dr. Siegfried Schloissnig, a 33-year-old Computer Scientist with a Doctorate in Human Biology, who previously worked as a PostDoc at the European Molecular Biology Laboratory (EMBL). A PostDoc and two PhD students will work under his leadership in Heidelberg.
The mentor: a pioneer in bioinformatics
Prof. Eugene “Gene” Myers, one of the pioneers in bioinformatics, is affiliated with the group as a mentor. The U.S. American developed the BLAST, the most widely-used search program in molecular biology, and wrote programs for whole-genome shotgun assembly that significantly contributed to the success of the Human Genome Project. The human genome was completely deciphered in the course of this project. Since June 2012, Gene Myers has been working as the director and “Klaus Tschira Chair” at the Center for Systems Biology in Dresden. The new center was established by the Max Planck Society in collaboration with the Klaus Tschira Foundation and the Max Planck Foundation. The center, which is a joint project of the Max Planck Institutes for Molecular Cell Biology and Genetics and for the Physics of Complex Systems, is set up to develop methods to better understand the cellular processes during the growth of an organism.

New approaches to the de novo assembly

The new junior research group at HITS will also work on these objectives in collaboration with Gene Myers’ laboratory in Dresden and the recently established Dresden Genome Center. Together with his group, Siegfried Schloissnig will develop new approaches to the so-called de novo assembly, which is the reconstruction of genome sequences by means of DNA sequencers and bioinformatic methods. In the course of sequencing by standard methods, DNA is copied multiple times. These copies are randomly split up into numerous small fragments. These fragments are examined for overlaps by means of bioinformatic methods and are subsequently reassembled. The smaller the fragments and the more complex the genome of interest, the more complicated is the problem. The situation becomes even more difficult, when no comparable genome is available and researchers have to assemble the genome de novo, i.e. anew. This is exactly the case with flatworms,  whose genetic codes the HITS junior group plans to decipher.

The jigsaw puzzle of flatworms

The scientists thus ventured into difficult terrain:  Until now the genomes of flatworms have been considered indecipherable because of their complex structure. “Two-thirds of the worm genome keep recurring,” explains Siegfried Schloissnig. “It´s like a jigsaw puzzle. And two-thirds of it are nearly identical white particles.” Together with the laboratory in Dresden, he will, for the first time, compare the currently available gene sequences of 12 worm species. The computational analysis will be performed at HITS. By means of new algorithms Dr. Schloissnig intends to piece together the DNA jigsaw puzzle of flatworms. Flatworms are masters of regeneration, and are, therefore, interesting for scientists: If they are cut in two pieces, each half will develop into a new worm. No animal is able to do it faster and more efficiently. “We’ll begin with studying Schmidtea mediterranea, which is the most interesting flatworm for Regenerative Medicine”, says Siegfried Schloissnig, “and then proceed with other species of this phylum.” By comparing the genetic material researchers hope to gain new insights into regeneration of tissue that could have a huge impact on medicine, for example, help developing methods to replace inoperative cells, tissues and organs with cultivated tissues or to stimulate endogenous regeneration and repair processes.
Computational Biology is the third research group at HITS, which uses mathematical methods and computer simulations to solve biological and medical problems. This year two more research groups will be established at the institute: The first one will deal with theoretical astrophysics and the second one with computational statistics. By 2014, HITS plans to comprise ten research groups as well as further research units such as junior groups and associated researchers.

Press Contact:
Dr. Peter Saueressig
Presse- und Öffentlichkeitsarbeit
HITS Heidelberger Institut für Theoretische Studien
Tel: +49-6221-533-245
Fax: +49-6221-533-298
peter.saueressig@h-its.org
https://www.h-its.org

Scientific Contact:
Dr. Siegfried Schloissnig
Junior Group Computational Biology
HITS Heidelberger Institut für Theoretische Studien
Tel: +49-6221-533-307
Fax: +49-6221-533-298
siegfried.schloissnig@h-its.org
https://www.h-its.org