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Medical Molecular Systems Biology

  • Vakcode 051 BMS
  • Part of the master program MECICAL BIOLOGY / MEDICAL BIOCHEMISTRY
  • The June part of the course will also be an elective for top Medical Students
  • Course coordinator: Prof. Dr. Stanley Brul Molecular Biology, Faculty of Science, Science Park s.brul@uva.nl 020-5256970 / 7079.
  • AMC coordinator: Dr. Rolf Boot Department of Medical Biochemistry AMC K111, r.g.boot@amc.uva.nl 020-5665157.

Background

Medical Biochemistry means the chemistry of life in health and disease. In the course Medical Biochemistry and Medical Molecular Systems Biology, the teachers will introduce you to a thorough understanding of how molecules take care of all the important chemical and cellular processes that occur during health and disease. The recurrent theme is integration: genetic, signal transduction and metabolic reactions form an integrated complex network of reactions that is at constant steady state (homeostasis) with its environment. Alterations like environmental stress / life style induced perturbations of homeostasis, mutations and polymorphisms in single molecules not only affect single chemical processes but also cellular behavior and can have a severe impact on the proper functioning of complete organs and the organism itself. Thus, studying biochemistry nowadays extends from genetics to genomics, proteomics and gene and protein networks, to metabolic networks of lipids, carbohydrates and proteins, to cellular communication and signaling cascades involved in complex disorders of organs and the cardiovascular circulation. The research tools used in modern biochemistry similarly span a wide range of techniques from genome-wide micro-arrays to metabolic profiling, to mass spectrometry of peptides, proteins and other bio-molecules. In most cases these studies are no longer performed in the test tube, but in complete cells, tissues or organisms, using genetic approaches like viral transductions, RNA-interference and knock-out or transgenic mice. Therefore, we have chosen a format for this course, in which you will cover all the major issues in medical biochemistry both at the textbook level, and at the forefront of biomedical research in a clinical setting. What we hope to accomplish is not for you to memorize detailed knowledge or books by heart, but to come to an integrated insight and understanding of the molecular basis of metabolism and disease processes, which will guide you through the multidisciplinary way in which modern day medical biochemical research is performed.


BMS051: Medical Molecular Systems Biology; Dealing with stress

The first part of the course is spent at the Swammerdam Institute of Life Sciences (SILS) of the Science Faculty (FNWI) of the University of Amsterdam. The location is Science Park (SP). In the mornings of the first week we will discuss how biology deals with stressful environments in bacteria, fungi, modelsystems and man. Students are divided in groups of maximally 4 and choose one of the five topics that are discussed in the first week. The topic is turned into a full application according to the guidelines of the Dutch Applied Science Council (STW) during the next 3 weeks. Each topic is introduced in morning lectures. In two afternoon sessions specific tools are discussed in more detail. In the 2nd week microscopy techniques and systems analysis tools are introduced in the mornings. In two afternoon sessions practical aspects are discussed. By the end of the second week students have a good comprehension of ways in which regulation of stress response can be analyzed at various levels of cellular organization.

In the 3rd week a Bioinformatics perspective is given from the clinic. Thus molecular systems biology is put (back) in a clinical setting. Students then get time to finalise a draft of their proposal and hand it in on the Wednesday of the third week to the relevant teacher and the group that will lead the discussion on the Friday afternoon of that week. There will be time for questions and answers with the course coordinator and in the afternoon there is a key-note lecture by a researcher who combines fundamental insight in (micro)biological behavior with excellent scoping for application. By Friday of the 3rd week the students will have prepared a presentation on their topic which they share in an afternoon session for discussion with the rest of the group and the lecturers. The group takes input from the respective lecturer as well as from the discussion session.

In the 4th week the Tuesday features a test examination. The examination will be open book and draws from topics of the first two weeks. Friday before the examination the, then final proposals according to STW format, can be handed in by e-mail.

Bioinformatics

  • Mo October 10th, 2011 (van Kampen: AMC / SILS)
  • Morning 11:00-13:00
  • HC: BioInformatics in a medical environment: structuring & analyzing the data deluge

Course material

Contact

Antoine van Kampen (a.h.vankampen@amc.uva.nl / 020-5667096 / 06-41768067)
Topic revision: r5 - 29 Sep 2014, PerryMoerland
 

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