fall_school_2012
Fall workshop in infection biology 2012 by the University of Würzburg
Autumn School / Summer School from Oct. 23 to Oct. 26, 2012
Fall Workshop / Fall School in Infection Biology 2012
University of Würzburg, Germany
October 23rd – 26th 2012
Modern Methods in Infection Biology
The University of Würzburg is listed amongst the top four German universities in the Life Sciences and has a strong focus on infection biology research (source:funding ranking DFG). Participants will learn about new methods, modern techniques, and cutting edge research. Important new methods in transcriptomics, drug screening, microscopy, and system biology will be discussed and demonstrated.
Goals
Participants will gain insight into important models of infectious diseases and modern research methods, as well as gaining a deeper understanding of specific subject areas.
Target group/selection criteria:
Outstanding Bachelor/Master students, in addition to PhD students. Applicants are selected on the basis of motivation and qualification. International applications are welcome, as are applications from outstanding students of the University of Würzburg.
This workshop presents a major opportunity for networking.
Attestation
Certificate of Participation
Language: English
Applications:
Application deadline: Sept 30th, 2012
Participant limit: 25 students
For application information please contact Dr. Ulrike Rapp-Galmiche at the following email address: ulrike.rapp-galmiche@uni-wuerzburg.de
Applications should include:
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letter of motivation (100 words) specifying focus of interest, reason for participation, and expectations
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curriculum vitae
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publications if applicable
A limited number of student stipends (accomodation, travel) will be available on a competitive basis.
Lecturers will lead the students through the latest techniques in infection biology including microscopy, RNAomics, system biology and drug screening. The organisms we will focus on include plasmodia, trypanosomes, staphylococci and further eubacteria.
File
Software required:
ActivePerl: http://www.activestate.com/activeperl?gclid=COqw-dfblrMCFYta3godwVwAcQ
BioPerl: http://bioperl.org/DIST
Blast: ftp://ftp.ncbi.nih.gov/blast/executables/release/LATEST/
Program
Workshop New Approaches in Infection Biology
October 23rd- Professor Dr. Dandekar
Bioinformatics
Location: Seminar room of biochemistry B108/109
You find that easily, if you start in the main hall or Foyer of the Biocentre of the University of Würzburg
https://www.biozentrum.uni-wuerzburg.de/en/about-the-biocenter/how-to-get-here//
If you have the lecture theatres A101 (big one) and A102 (medium one) in your back, you just
turn right, go up the stairs to biochemistry and follow the signs (“workshop, new approaches in infection biology), then you reach the seminar room in B-section of the building, room B108/109.
Begin: 9:00
Equipment: notebooks – these are provided (CIP pool and our seminar room is already used by courses, e.g. F2 Bioinformatics and scientific training for the biology teacher students)
Introduction: Systems biology of infection – bioinformatical approaches
Prof. Thomas Dandekar 9:00-10:00
Part I Genome analysis and annotation 10-11:00
Prof. Thomas Dandekar (basics and challenges of sequence analysis; Annotation and pathway alignment; Comparative genomics)
Part II Databanks and Ressources 11-12:30
Dr. Chunguang Liang (Protecs database, EcoliHub / MetaCyc, COGs etc.)
Lunch break 12:30-13:30
Part III Modelling metabolic networks 13:30-15:00
Astrid Fieselmann (how to do elementary mode analysis; simple examples on Staphylococci from own research)
Coffee break 15:00-15:30
Part IV Signalling in infectious biology 15:30-17:00
Dr. Muhammad Naseem (using Squad, gene expression data, semi-quantitative models)
Part V Current trends in systems biology in infectious biology
Prof. Thomas Dandekar 17:00-18:00
(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)
Workshop New Approaches in Infection Biology
October 24th- Dr. Susanne Kramer
Trypanosomes
Location: Seminar room of biochemistry, B108/109
Begin: 9:00
The African trypanosome: a killer and a survival genius
This course will introduce you to the unusual biology of the African trypanosome. You will explore three features that largely contribute to the parasites pathogenity (antigenic variation, antibody clearance, resistance to the trypanolytic factor) in teams and you will present your results in a rather non-conventional way (by pantomine).
9:00-9:45 Introduction lecture to Trypanosomes
9:45-10:30 Movie (African sleeping sickness)
10:30-11:00 Coffee break
11:00-12:30 Reading time / research time for pantomine
12:30-13:30 lunch break
13:30-14:30 Current Research in Würzburg trypanosome labs: PhD students report
14:30-16:30 Team discussions, preparing the pantomine (Coffee break in between)
16:30-17:30 Pantomine
Workshop New Approaches in Infection Biology
October 25th- Dr. Martin Fraunholz
Staphylococci
Location: Lecture Seminar room of biochemistry, B108/109
Lab Department of Microbiology, Room C235
Introduction
Phagosomal escape of Staphylococcus aureus
Principles of Confocal Laser Scanning Microscopy
Image analysis of fluorescent micrographs and other imaging data using ImageJ/Fiji
images: visualization and manipulation (Background subtraction, Brightness & Contrast)
particle counting
multi-dimensional images
Images stacks and stack manipulation (Aligning stacks slices, measuring intensities over time)
Image Montages
Experimental part: Phagosomal escape of S. aureus (on a Leica TCS SP5, Room C235; smaller groups)
Students can bring their own laptops and do image analysis with their own data as well.
Topics:
Station 1: PD Dr. Gabriele Pradel
Confocal laser scanning microscopy: Imaging targets of transmission blocking vaccines.
Station 2: Ludmilla Sologub
Giemsa staining: Identifying P. falciparum blood stages in blood smears.
Station 3: Dr. Matthias Scheuermayer
Insectary: Dissecting Anopheles stephensi mosquitoes.
Station 4: Selina Kern
Malstat assay: Screening drugs in the P. falciparum blood stages.
Station 5: Andreas von Bohl
Exflagellation inhibition assay: Evaluating the effect of drugs on gametogenesis.
