Slime mold, naked mole rat, sequence data analysis

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Dr. Karol Szafranski celebrates his 25th anniversary at the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) Jena. This milestone prompts us to look back on the various stages of his career.

Jena. 25 years in the service of research are nothing unusual, but 25 years in the service of a single research institute is. Dr. Karol Szafranski has reached this anniversary at the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) and looks back on his professional career with pleasure.

The 54-year-old grew up in Schleswig-Holstein. After completing his biology studies with a focus on botany in Düsseldorf, he came to Jena in 1998 to do his doctorate at the university and at the FLI under Prof. André Rosenthal. At that time, the FLI, then known as IMB (Institute of Molecular Biotechnology), was actively involved in the so-called Human Genome Project. "Jena made the largest German contribution to the genome project. This is perhaps not as widely recognized today," Szafranski notes, adding: "The human genome project and the mouse genome project paved the way for current projects”. As a doctoral student, he was part of the team that decoded the genome of the slime mold Dictyostelium discoideum, a single-cell organism (social amoeba) used as a model for cellular movement within a multicellular network.

After completing his doctorate, Szafranski continued to work at the institute with Dr. Matthias Platzer in the Jena Centre for Bioinformatics (JCB) project, an exchange network for various research groups in Jena. "Our focus until 2004 was on gene regulation via promoters," the biologist explains.

The postdoctoral researcher then spent almost a year at the Center for Bioinformatics at the University of Pensylvania in Philadelphia.There he worked on the recognition of micro-RNAs in the genome. "It was an exciting time to soak up the academic atmosphere in America. However, staying long-term was not an option for me," says Dr. Karol Szafranski.

In 2005, the scientist returned to Jena to join PD Dr. Platzer research group, only the institute was now called the Leibniz Institute on Aging - Fritz Lipmann Institute (FLI). At the time, the group was working in the National Genome Research Network (NGFN), a large-scale biomedical research program based on the Human Genome Project. "A technology that significantly changed our work was next-generation sequencing, which was introduced at the FLI around 2009," Szafranski reports. This technology provides extensive sequence information from biological samples at low cost and is still shaping molecular genetic research today.

This was followed by a research project aimed at identifying molecular networks responsible for a long and healthy life. This was funded by the Leibniz Association and - in collaboration with the Leibniz Institute for Zoo and Wildlife Research (IZW) Berlin - focused on naked mole rats (Heterocephalus glaber), a long-lived animal model.

The mouse-sized rodents not only have an extremely long lifespan, but also enjoy a an exceptionally long period of good health, as they do not suffer from age-related diseases. In a second, subsequent DFG project on related gray mole-rats, it was found that longevity is also linked to the social status of the individual animal. These mole-rat species, which live underground in the semi-deserts of East African, have developed remarkable strategies for long, healthy ageing. "Slow development, frugality (keyword: dietary restriction) and low stress contribute to a longer life," Szafranski summarizes the findings. When he talks about these peculiar mammals, he almost becomes enthusiastic: "I really enjoyed these research projects, especially the close work with the cooperation partners and the doctoral students on site. The research goals and results were very easy to communicate to a broad audience."

When asked about the highlight of his career so far, the biologist mentions the transition from researcher to Core Facility Manager a few years ago. "It was a radical step that I have never regretted," Szafranski says. Initially, he was manager of the "Bioinformatics" core facility (CF for short), which later incorporated "Scientific IT" and became CF "Life Science Computing". This service facility supports the FLI scientists when the analysis of experimental data requires complex algorithms, advanced statistics or high computational power for processing. The main focus is on the analysis of sequence data generated by other core facilities (CF Next Generation Sequencing, CF Proteomics or CF Functional Genomics). A very challenging project was the introduction of an electronic laboratory notebook, says the CF Manager, summarizes his team’s work. Equally important was the development of an HSM system (Hierarchical Storage Management) for long-term data storage.

He was surprised by how many aspects were added to his scientific role as a CF Manager. He had not expected the work with a fixed team, the increased (personnel) responsibility, and the significant creative freedom. His occasional involvement in the works council and his work as a person of trust added more facets on a human level that he enjoyed. The exchange with all colleagues is very important to him.

His insight from the diverse projects with various research groups: the more precisely a goal is defined, the easier the offered analyses can contribute to research progress. Project meetings are therefore a key part of the role. "From my own time in the lab, I know that there is painstaking work behind the experimental data. I hope the CF users feel our appreciation for the 'grapes' they entrust to us for refinement," says Karol Szafranski.

In the early years of working in the Core Facility, there was a lack of time to pursue his own research ideas. With the addition of a new colleague to his team, this is now within reach. "Bioinformatic method development is being consolidated, systematically advanced and tested, so that independent scientific publications are also on the horizon," Szafranski concludes.

In his free time, Dr. Szafranski seeks balance in activities that allow him to switch off his mind, such as a weekly hobby dance class or tending to his balcony plants: "This year, for example, I'm growing two varieties of chilli for the kitchen."

We would like to thank Dr. Karol Szafranski for his work at the FLI and wish him all the best and much success in the implementation with all the projects that lie ahead for him and his team.