Chair of Bioinformatics

    Program details_2017

    Program details

    Lectures and labs will be held daily from 9.00 a.m. to 5.15 p.m. The main meeting point is lecture theatre A102.

    Monday September 18th

    Systems Biology of Infection

    Lecturer: Prof. Dr. Thomas Dandekar (Homepage)

    Chair, Bioinformatics

    Pseudomonas Syringae attacks the host -- how do you understand the host response?
    (A) Phenotype: Pst (104 CFU/ml) infection; red arrows indicate pathogen inoculation; black arrow indicates mock (10mM MgCl2) inoculation. Symptoms weare photographed three days post pathogen inoculation (DPPI). (B) Network: Topology of Pst- mediated hormone disease networks in Arabidopsis. Connectivity among nodes is based either on activation (->) or inhibition (-|). Node designation: blue, enzymes of hormone biosynthesis and degradation; yellow, active hormone molecules; green, host regulatory factors; red, Pst- originated pathogenicity factors responsible for triggering immunity in Arabidopsis; pink, “PR-1”, marker node for immunity against the infection of Pst in Arabidopsis. All nodes are denoted by abbreviations.
    More information on these questions is found in our plant cell paper: Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, Dandekar T. Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin. Plant Cell. 2012 May;24(5):1793-814.
    However, the same techniques can also be applied (and are shown in the course) to study human infection defense against pathogens. 


    Location: lecture theatre A102 and CIP pool, You find that easily, if you are in the main hall or Foyer of the Biocentre of the University of Würzburg

    Equipment: computers – these are provided (CIP pool)

    09:00-10:00 Introduction: Prof. Thomas Dandekar, Department of Bioinformatics University of Würzburg (chair) and EMBL Heidelberg
    Title: "Systems biology of infection – bioinformatical approaches" (lecture theatre  A102)

    Including administration: attendance, insurance

    10:00-11:30 Part I Databanks and Resources (CIP pool in the basement, we will lead you to it if not yet known)

    11:30-14:15 Part II Getting into -omics: transcriptomics and proteomics (lecture theatre A102)

    • 11:30-12:30 Dr. Konrad Förstner, Institute for Molecular Infection Biology, University of Würzburg
      Title: "Dual RNA sequencing in infection biology"

    12:30-13:30 Lunch break

    • 13:30-14:00 Dr. Elena Bencúrová,  Laboratory of Biomedicine, Microbiology and Immunology,
      University of Veterinary Medicine and Pharmacy in Kosice, Slovakia and University of Würzburg
      Title: "Proteomics in infection biology"
    • 14:00-14:15 Discussion

    14:15-14:30 Break

    14:30-16:00 Part III Current trends in systems biology (lecture theatre A102) 

    • Prof. Thomas Dandekar (we will show and discuss current trends in systems biology with a focus on computer-based approaches, what they can and what they can not elucidate)
    • Prof. Alicia Ponte-Sucre, Humboldt professor, Insituto de Medicina Experimental, Universidad Central de Venezuela, Caracas
      Title: "TICS, surveillance and prevention in neglected diseases and their relation with the sustainable and millennium goals"

    16:00-16:30 Coffee break

    16:30-18:00 Part IV Drug design and signalling in infection biology (CIP pool)

    • Dr. Muhammad Naseem, Bogazici University Istanbul, Turkey and University of Würzburg
      Title: "Using Squad, gene expression data, semi-quantitative models, in essence the cell paper"
    • Dr. Sergey Shityakov, Department of Anaesthesia and Critical Care, University Hospitals of Würzburg
      Title: "Drug design in infection biology"
      Rational drug design and discovery of novel antibacterial compounds using linear interaction energy (LIE) method

    Useful link:


    19:00 Welcome Dinner  

    Tuesday September 19th

    Intracellular S. aureus

    Lecturer: Dr. M. Fraunholz (Homepage)

    Microbiology (Lectures: A102; Practicals: CIP pool)

    Figure: Staphylococcus aureus (cyan) in phagolysosomes of human cells (yellow)

    Topic area: Microscopic analysis of intracellular bacterial host-pathogen interactions: Practical image analysis with Fiji/ImageJ (basics & motion tracking, feature counting)

    Upon infection Staphylococcus aureus is readily phagocytosed by macrophages and neutrophils but is also to invade epithelial and endothelial cells, fibroblast, osteoblasts, and keratinocytes. The uptake by latter so-called non-professional phagocytes has been proposed to play a role in evasion of the innate immune system. Further survival of phagolysosomal killing by S. aureus may also lead to disseminating infections within migrating phagocytes. We and others have shown that S. aureus is capable of escaping from host cell phagosomes. One of our methods is microscopy based and relies on the recruitment of a cytoplasmically expressed host cell marker that is recruited to the bacterial cell wall upon phagosomal membrane rupture.

    On the second day of the summer school we will address theoretical and practical aspects of confocal laser scanning microscopy as well as the underlying fluorophores. We will analyze images of uninfected and infected human cells using Fiji/ImageJ, a tool which is handy for other image analysis aspects, too.

    Participants should bring a USB Thumb drive, if they want to keep their own personalized ImageJ version.

    Location: CIP Pool in the basement

    Wednesday September 20th

    Location: Lecture Theatre A102

     8:30 Introduction Prof. Dandekar
     8:35 Lecture Prof. Thilo Figge (Jena) and Prof. Oliver Kurzai (Jena/Würzburg)
                          on Fungal infections and modelling by agent based simulations
    10:00 Lecture Prof. Florian Erhard (Virology, Würzburg)
                          on Systems-Virology
    11:00 Uhr meet international students of the university of Wuerzburg
    11:30 Uhr Guided Tour on 3D tissue models in infection
                (guide: Sebastian Häusner) to visit the laboratory of
                Prof. Heike Walles on 3D tissue models at Röntgen-Ring 11

    Lunch and free time
    16:00 tour of residence 

    Thursday September 21st

    Trypanosomes (Lectures, practical: A102)

    Lecturer: Dr. S. Kramer (Homepage)

    Zoology I

    The African Trypanosome: A killer and a survival genius

    African trypanosomes cause African Sleeping Sickness as well as the related cattle disease Nagana, affecting people’s health both directly and indirectly in sub-saharan Africa. During the ‘Trypanosome-day’ of the summerschool we will look at the parasites from the point of view of a parasitologist, but also from the point of view of a cell biologist: you will see that trypanosomes are model organisms for many biological questions. A non-conventional teaching method will be used to explore the non-conventional biology of trypanosomes: Pantomine. We will also have a look at the ‘real beast’ by high resolution microscopy and we will gain an insight view into the actual research that is currently taking place in the trypanosome labs that are settled in Würzburg.


    Location: Lecture Theatre A102

    9:00-10:30 Introduction lecture (Trypanosomes) and safety instructions (Susanne Kramer)

    10:30-10:45 Coffee break

    10:45-11:15 Movie (African Sleeping sickness) + discussion (Susanne Kramer)

    11:15-11:45 Current research projects in Würzburg, PhD student reports

    • Nicole Eisenhuth
    • Erick Aroko

    11:45-12:15 How to do work with Tsetse flies (discussion with Dr. Ines Subota)

    12:15-13:15 Lunch break

    13:15-14:00 Invited Guest speaker Prof. Christian Janzen: life cycle regulation in trypanosomes

    14:15-15:00 Invited Guest speaker Prof. Alicia Ponte Sucro: Leishmaniasis and drug resistance

    15:00-17:00 Preparation Pantomime (Susanne Kramer and Brooke Morriswood) 

                           Life cell imaging of trypanosomes (Sarah Schuster) in small groups

    17:00-17:30 Pantomime presentations

    Friday September 22nd

    Parasitic Helminths

    Lecturer: Prof. Dr. K. Brehm (Homepage)

    Medical Parasitology

    Institute of Hygiene and Microbiology

    Figure: Echinokokkus

    On the first day of the workshop the labs and lectures will not be at the Biocentre but at the University Clinics Department Hygiene and Microbiology (Haus E1).

    Please find the written directions and maps below: 

    (please click the pictures to enlarge them)

    You can reach the main area of the University Hospital with the streetcar routes 1 and 5. You get on the streetcar at the Hautpbahnhof Ost (Main Station East) in the direction of Grombühl and get off at stop “Uniklinikum Bereich D (University Hospital area D; Petrinistrasse)". You can reach the Institute of Hygiene and Microbiology by walk (5 min) as indicated on the map. (The walk from the Main Station takes about 20-25 minutes.)

    Parasitic Flatworms: A tale of mortality and immortality.

    Parasitic helminths are a major cause of so-called ‘Neglected Diseases’. And Neglected Diseases are called ‘neglected’ because nobody (or only very few) has/have an interest to study them. So, why are we doing it? This is something we’re going to figure out in the ‘Parasitic Helminth’-day of the summer school. We shall learn that the development of novel therapies is not the only motivation to do infectious disease research and that these parasites (like many others) are highly fascinating from the view-point of immunologists as well as cell-, developmental- and evolutionary biologists. Above all, we shall learn how molecular research can be done in a ‘non-mainstream’ setting and which strategies should be followed to establish an infectious disease model system from scratch.


    9:00-10:30 Introduction: Parasitic helminths and the spellbinding world of tapeworm infections (including tapeworm movie; demonstration of specimen; narration of the ultimate tapeworm joke)

    10:30-10:50 Coffee break

    10:50-12:00 Interactive Teaching: how to develop a research model system from scratch.

    12:00-13:00 Lunch break

    13:00-14:20 Würzburg’s current tapeworm research projects: PhD students report

    14:20-15:50 Practical aspects of tapeworm and larval tapeworm research (in small groups)

    15:50-16:10 Coffee break

    16:10-18:00 Final discussion (including Quiz Show ‚Who wants to be a Parasitonaire?‘)

    19:00 Farewell Dinner