News 2019

Bacteria of the species Escherichia coli live in the human gut as non-pathogenic commensals. However, if these bacteria acquire virulence factors they can cause severe intestinal and extraintestinal diseases. Pathogenic E. coli are classified into pathogroups based on characteristic virulence factors. Recent studies documented, however, the emergence and clinical significance of hybrid E. coli strains that possess virulence factors from more than one pathogroup.
EvoPAD researchers Noble Selasi Gati, Ulrich Dobrindt and Alexander Mellmann now published a study unravelling the diversity of virulence genes and the origin and evolution of a hybrid E. coli genotype. Using a comprehensive whole genome sequencing dataset of all collected E. coli strains of multilocus sequence type 141 (ST141) the authors showed that the majority of strains possess virulence factors from both intestinal and extraintestinal pathogenic E. coli. In addition, evolutionary analyses revealed that ST141 E. coli serve as a ‘melting pot’ for pathogroup conversion via the addition and exchange of virulence factors from various pathogroups. The results support an alternative view of pathogen emergence where - in contrast to the classical theory of pathogen emergence where virulence factors are acquired sequentially and linearly - E. coli pathogroups can undergo phased metamorphosis into one another. The study will be published in the January issue of the Journal of Clinical Microbiology and is already available online.

Original article: Gati NS, Middendorf-Bauchart B, Bletz S, Dobrindt U & Mellmann A (2019) Origin and evolution of hybrid Shiga toxin-producing and uropathogenic (STEC/UPEC) Escherichia coli of sequencing type 141. Journal of Clinical Microbiology [epub ahead of print]
 

The spread of antibiotic resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA) pose a major issue in public health. Regular exposure to livestock, especially swine, leads to a high frequency of livestock-associated MRSA colonization in humans such as pig farmers posing an increased risk for developing severe infections in these persons. A new study by EvoPAD researchers Natalie Effelsberg, Sergej Udarcev and Alexander Mellmann published in the Journal of Clinical Microbiology shows that while livestock-associated MRSA are detected also in humans with occasional contact to livestock these colonisations are temporary rather than persistent. Additionally, results from the study indicate that the prevalent livestock-associated MRSA lineage CC398 originated in Western Germany in the late 1990s. For their analyses, the researchers submitted isolates from scientists visiting pigsties for fieldwork, as well as corresponding isolates from pigs and environments of the visited farms in the Westphalia region in Western Germany to whole genome sequencing.

Original article: Effelsberg N, Udarcev S, Müller H, Kobusch I, Linnemann S, Boelhauve M, Köck R & Mellmann A (2019) Genotypic characterization of livestock-associated methicillin-resistant Staphylococcus aureus isolates of clonal complex 398 in pigsty visitors: transient carriage or persistence? Journal of Clinical Microbiology 58:e01276-19.
 

In many eukaryotes, bits of the germline DNA are removed during germline-soma differentiation to form a soma-specific genome in a process called DNA elimination. Inaccurate or inefficient DNA elimination may contribute to genotypic diversification in clonal cells. EvoPAD researchers Valerio Vitali, Rebecca Hagen and Francesco Catania now published a study in Genome Research investigating the impact of ecological changes on the robustness of programmed DNA elimination. Results from their research show that germline-soma differentiation in the ciliate Paramecium tetraurelia is affected by changes in the environmental temperature. Following sexual reproduction, P. tetraurelia eliminates 25% of its DNA from the germline genome to form a functional somatic copy. Exposure to sub-optimal culturing conditions reduced the efficiency of programmed DNA elimination, giving rise to variation in the somatic genome. This variation was associated with changes in gene expression and likely carried forward to the sexual offspring, thus potentially representing a substrate for microevolutionary processes. The study uncovered a direct link between ecological changes and somatic DNA variability, a process that could underlie adaptive plasticity in genetically identical cells.

Original article: Vitali V, Hagen R & Catania F (2019) Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia. Genome Research 10:1693-1704.
 

From 10 – 13 September 2019, EvoPAD held its third summer school, which focussed on bioinformatics. The summer school took place at the K6 seminar hotel in Halberstadt in the Harz region. It brought together the EvoPAD PhD students with three of the EvoPAD PIs in an interactive learning and teaching environment. Dr Victoria Shabardina and Felix Manske from the Institute of Bioinformatics at the University Hospital Münster joined the group as external experts. During the summer school, the PhD students went through the whole process of generating and analysing next-generation sequencing data, from isolating the DNA to analysing the data. A big part of the teaching was done by students with experience in data analyses, teaching their peers. Besides practicals, listening to talks, presenting, and discussing research, the group also enjoyed some leisure time, e.g. during an excursion to the Teufelsmauer.

From 27-30 August 2019, EvoPAD PhD students completed a seminar on Philosophy of Biology. The 4-day programme was taught by Dr Fridolin Groß from the Institute of Philosophy at the University of Kassel.

From 9 June - 10 July 2019, Mercator Fellow Thomas Flatt completed his second on-site stay with EvoPAD. During his time in Münster, he gave a lecture on "New Horizons of Ageing" and was involved in teaching a part on scientific writing and the publishing process within the EvoPAD course "From experimental design to publishing". Moreover, he met with several graduate students to discuss their research. We thank Thomas Flatt for his continuing commitment in EvoPAD and look forward to ongoing collaborations and his future visits in Münster.

Thomas Flatt is a full professor of evolutionary biology at the Department of Biology at the University of Fribourg in Switzerland. His research addresses fundamental questions in evolutionary genetics of adaptation, life-history evolution, the evolution and mechanisms of aging and longevity, and phenotypic plasticity. He has been a Mercator Fellow of EvoPAD since May 2018 and visited Münster for his first stay in June/July 2018 as well as for a short visit in February 2019.
 

What is ethics of science? What is scientific freedom and the role of science in society? EvoPAD PhD students now completed a seminar focussing on these questions supplemented by detailed case studies on e.g. CRISPR/Cas9 and heritable human genome editing, climate change and climate change denial, anti-vaccinationism, and creationism & Intelligent Design. The 3-day programme was taught by Alexander Christian from the Department of Philosophy at the University of Düsseldorf.

On 21-22 February 2019 thirty PhD students, postdocs and PIs met for a workshop focusing on experimental evolution organized by EvoPAD PhD students Nina Kranke and Ana Lindeza. On the first day, keynote speakers Claudia Fricke (University of Münster), Eric Desjardins (Western University, CA), Thomas Flatt (EvoPAD Mercator Fellow, University of Fribourg, CH), and Henrique Teotónio (University of Paris, FR) presented concepts, examples, challenges in experimental design, omics technologies for analyses and philosophical aspects of experimental evolution. The talks were followed by a poster session where graduate students presented and discussed their projects with the keynote speakers and other participants. On the second day, the participants gathered in small groups to discuss appropriate controlling of experimental evolution experiments, the use of genonimcs vs. transcriptomics as analysis tools in experimental evolution and external validity. At the end of the workshop, the participants concluded that the workshop was resoundingly successful and provided valuable insights on planning and running an experimental evolution project. The programme of the workshop can be downloaded here.

Presenting research in concise, interesting and convincing publications represents a challenge for many scientists. Yet, since success in the academic field is highly dependent on successful publication, formal training in scientific writing provides an excellent opportunity to learn scientific writing essentials. On 29-30 January 2019 EvoPAD PhD students completed a course on scientific writing taught by Dr. Melanie Conrad from the Charité Berlin. The course comprised lectures and interactive exercises on general writing guidelines and the challenges and requirements of scientific writing. A PhD student commented after the workshop: "This should be a compulsory workshop for PhD students in biology. I think it would be helpful in any stage of their PhD."