First JSMC Summer School 2025

August 1-15, 2025

What is the Summer School and its Program?

This year, we will host the first Summer School at our graduate school in Jena. We crafted an engaging two-week program with scientific modules, lectures, a workshop, and social events (e.g. night hike, Midsummer party, etc.). Additionally, the scientific program will offer selected candidates the opportunity of on-site visits to the Bio-Science industry in and around Jena, participate in lectures on state-of-the-art live-cell imaging with our collaborators from overseas, and get in touch with PhD representatives and spokespersons of our graduate school as well as getting the opportunity to chat with research group leaders and industry professionals alike.

What does the Summer School package include?

The JSMC will financially support accommodations including dinners, and partial travel expenses for all selected participants. Guided tours in and around Jena, the institutes, campuses, and tickets for public transport will also be part of the Summer School package.

Who can apply?

Applications are open to national and international MSc. graduates in biosciences, biochemistry, bioinformatics, or related fields who are interested in pursuing a doctorate in Microbial Communication.

How to apply?

To apply for the Summer School please follow the link and fill out the online application form by April 30^th. Please indicate which offers you would like to participate in. Please note that, if selected, the final program of the JSMC Summer School 2025 will be crafted individually for you but may differ from your preferences as it is subject to the availability of free spots.

Please find the schedule as well as a detailed description of the program below.

Prof. Dr. Maria Mittag, Matthias Schleiden Institute of Genetics

The module aims to introduce participants to the role of calcium ions (Ca²⁺) as an important secondary messenger. It provides a theoretical background on Ca²⁺ signaling in green alga as well as in land plants and the human brain. Practically, the biflagellate alga Chlamydomonas reinhardtii will be used for the studies. Participants will learn to measure cytosolic Ca²⁺ transients using the luminescence-based apo-aequorin reporter assay along with a luminometer. Through hands-on training, participants will apply the apo-aequorin-based assay to detect and quantify Ca²⁺ dynamics and analyze the effects of abiotic stresses (such as pH shock and salt stress) and biotic stresses (such as bacterial toxins like orfamide A) on calcium signaling in C. reinhardtii. Participants will also examine which stressors result in deflagellation and thus immobilization of the algal cells.

Prof. Dr. Jan Schirawski, Matthias Schleiden Institute

Sporisorium reilianum f.sp. zeae is a biotrophic fungal pathogen that causes head smut disease in maize. Amongst the various symptoms observed in Zea mays upon infection, such as phyllody in male and female organs and formation of spores in tassel and cob, the formation of subapical ears is of prime interest. Using comparative genomics and deletion studies, the fungal effector protein SAD1 (SUPPRESSER OF APICAL DOMINANCE 1) was identified to be responsible for the formation of sub-apical ears. Localization studies and identification of the potential interaction partners of the effector protein in planta can provide valuable insights into its mode of action in plants. Preliminary studies suggest that SAD1 is secreted into the plant tissues upon infection and might be localized in both nucleus and cytoplasm of the host cells. To determine the functional relevance of localization of SAD1, plasmids containing NES-, mNES-, NLS-, mNLS-, and membrane-tagged versions of GFP fused SAD1 were constructed and subsequently used to transform Agrobacterium tumefaciens.

This module aims to verify the expression and localization of tagged SAD1 variants through A. tumefaciens-mediated transient expression in Nicotiana benthamiana, utilizing fluorescence microscopy. Additionally, it aims to immunoprecipitate the effector protein from infiltrated leaves and validate its presence via Western blotting.

Dr. Kathrin Fröhlich, Institute of Microbiology and Dr. Matthew Blango, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute

The isolation of ribonucleic acid (RNA) is a key tool for the molecular biologist. In the classical sense, RNA is involved as the messenger carrying information between DNA and proteins, but it also can act as an enzyme, regulate gene expression, facilitate translation, and be modified to expand its functional capacity further. If the RNA world hypothesis is correct, self-replicating RNA molecules may have even preceded DNA and protein on Earth! In the study of host-pathogen interactions, RNA has been shown to play an important role in the regulation of gene expression in both host and pathogen, but it also traffics between cells, for example from pathogen to host or between cells of the host to coordinate the host response to infection. This short module is meant to introduce the budding scientist to the exciting field of RNA research by highlighting various aspects of its most important technique, RNA isolation. By isolating high-quality RNA, the molecular biologist gains access to a variety of downstream assays, including direct assessment of particular RNA species or modifications, investigation of RNA structure or enzymatic activity, and measurement of gene expression using techniques like RNA-seq or reverse-transcription quantitative PCR (RT-qPCR). Research building from the study of RNA has led to vaccines, therapeutic targets, and is even being investigated for its potential in diagnostics.

Prof. Dr. Birgitta König-Ries, FUSION group

In this module, we will introduce basic principles and concepts of Research Data Management and provide hands-on experience with tools and practical recommendations for RDM in microbiology. The introductory interactive lecture will be followed by workshops on the electronic lab notebook eLabFTW, microscopy data management with OMERO, and the metadata management platform BEXIS2. Participants are advised to bring the data generated in the previous experimental modules.

Prof. Dr. Rosalind Allen, Theoretical Microbial Ecology Group

High throughput microplate data on microbial growth (i.e. growth curves) is increasingly routinely used to assess microbial response to different environmental conditions, including for example antibiotics. Yet to fully utilize this kind of data we need to extract quantitative information such as growth or killing rates. This short practical module will introduce students to software that has been developed in our group, that can be used to extract growth and killing rates from microplate growth curve data. Example datasets will be supplied. The module was tested in 2024 as part of the MMB003 course for microbiology master students at Friedrich Schiller University.

Prof. Dr. Christian Eggeling, Microverse Imaging Center

In this module, we will give an overview of the microscopy activities at the Microverse Imaging Centre. We will start with a general introduction to fluorescence microscopy and describe basic methods. Then we will present our equipment and briefly explain the more advanced microscopy modalities that we work with. Finally, we will present the Microverse Imaging Centre and give some examples of projects performed here. Hence, the participants will be informed about our offers: the possibility to get access to these high-end microscopes during their PhD program, get trained and guided for their imaging projects, and attend microscopy classes.

Dr. Clara Correia-Melo, Dr. Melike Donertas, Dr. Dario Valenzano and Dr. Katarzyna Winek, Leibniz Institute on Aging - Fritz Lipmann Institute

This module explores microbial communication within the context of host-microbiome interactions during aging, focusing on how microbial communities and their signalling influence host health over time. As organisms age, the composition and functionality of the microbiome shift, often contributing to immune system dysregulation, metabolic changes, and increased susceptibility to chronic diseases. This course will provide an overview of the recent research highlights on how aging impacts host-microbiome communication and how alterations in the microbiome may either accelerate or alleviate age-related decline. From a practical perspective, we will use a vertebrate aging model, the killifish and examine microbiome composition and host metabolic changes in young and aged individuals.  The module includes hands-on-experience from sample collection gut-microbiome composition analysis (nanopore sequencing), metabolic profile of microbiome and host-tissues using metabolomics, to computational analysis.

Dr. Annika Bartsch, Career consulting for academics

For many scientists, writing job applications tends to be quite difficult, especially for jobs in a competitive field. In fact, misunderstandings and mistakes in their application dossiers often prevent them from securing jobs for which they are perfectly qualified. This workshop will help you write a convincing application for the German academic job market.

Dr. Francois Olivier, Monash University, Melbourne, Australia

Date:  6.8.2025, via Zoom

Dr. Francois Olivier - Research Fellow at Traven Lab | fun.qi tools from Monash University, Melbourne, Australia will give a lecture on ‘Using live-cell imaging to resolve dynamic host-pathogen interactions’.

Dr Darren Thomson, Medical Research Council Centre for Medical Mycology at the University of Exeter

Date:  15.8.2025 11 am at HKI-lecture hall

Dr. Darren Thomson - Senior Experimental Officer |Medical Research Council Centre for Medical Mycology at the University of Exeter will give a lecture on ‘State-of-the-art microscopy techniques to study biology of human fungal pathogens’.

An afternoon at BLINK AG with presentations, coffee, and chats with scientists at their bench at BLINK.

‘At BLINK we are motivated by the desire to create innovative and accessible products that make complex assays simple to use across the entire bioanalytical continuum. Our long-term goal is to make meaningful and sustainable improvements in the fields of life science research, biotechnology, environmental testing, agriculture, veterinary medicine, and in-vitro-diagnostics.’