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Systems Biology for System Engineers

Division of Information Coding welcomes you to the following seminar series on Systems and Developmental Biology. The seminar series will give an introduction to the biological mechanisms that influence cell fate decisions during development, and will give examples of how system theory can be used to model these complex events. The series will feature invited talks.

Wednesdays (and Friday May 11) 13.15–15.00
March 28, April 4, April 11, April 18, April 25, May 11, May 16 and May 23
Locations:
March 28 and May 11: Systemet, Hus B, 2nd floor, entrance 27
Other lectures: Algoritmen, Hus B, 1st floor, between entrance 27 and 29.

Preliminary plan
  • 1. Introduction (The biological cell, the genetic code, cell lineages), March 28 - Robert Forchheimer (pdf)
    Abstract: In this introductory seminar I will give a brief overview of developmental biology. The biological cell and the genetic code will be described. The basic principles behind gene regulatory networks will be presented. Multicellular organisms are formed from cell divisions and some of the mechanisms will be touched upon such as asymmetric division, differentiation and control of 3D structure.
  • 2. From genes to functions (Gene regulation and transcription), April 4 - Sofia Pettersson (pdf)
    Abstract: This week's seminar concerns the process of converting the genetic code to the RNA segments and proteins that carry out the wide variety of tasks in living organisms. We will take a closer look at the processes of transcription and translation, and discuss some of the control mechanisms that affect these events. Transcription factors, signaling cascades and gene regulatory networks will be discussed, with examples of how they work to specify different cell fates in developmental biology.
  • 3. Cell biology (Cellular processes), April 11 - Sofia Pettersson (pdf)
    Abstract: This week's seminar will focus on cell biology and cellular processes. The seminar will cover the basic structure of animal cells and will highlight some specific processes, such as the various stages of cell division. In addition, the various mechanisms by which cells interact with and respond to their extracellular environment will be addressed. We will also revisit last week's topic by looking at how these events can initiate and affect gene transcription.
  • (Extra) Modeling the brain (Understanding the central nervous system in an information processing context), Apr 18 - Christer Svensson (pdf)
    Abstract: I try to give a personal view of the brain, from the perspective of physics and information technology. I describe well known basics regarding neurons and then continue with a systems oriented model, based on a couple of hypotheses emanating from 1973-2007. The main objective is to understand the function of the central nervous system through a reasonable model. Also some consequences of such a model are briefly discussed.
  • 4. Synthetic biology (IGEM-­-2011/Team Uppsala), April 25 - Erik Gullberg, Uppsala University (Invited speaker) (pdf)
    Abstract: This seminar will focus on prokaryotic synthetic biology. Synthetic biology is a young research field that applies the principles of engineering on biological systems to construct novel biological parts, design genetic circuits and "reprogram" organisms. Recent advances in DNA sequencing, gene synthesis and modelling of biological pathways have provided us with the tools needed to design and construct complex novel biological machineries, but our ability to reliably predict the behaviour of such systems is still limited. Standardization and better characterization of biological parts are important steps for making synthetic biology a more mature engineering discipline.
  • 5. Models for cell and organism development (ODE- and PDE-models and Boolean models), May 11 - Jan-Åke Larsson
    Abstract: In this seminar I will give a brief overview of mathematical models in developmental biology. I will cover the main model types (graph/dynamic, Boolean/continuous, deterministic/stochastic) and their basic properties, difficulties, and areas of usage. I will also give some examples from modeling in Drosophila (the fruit fly) and C elegans (a small roundworm).
  • 6. C. elegans - a model organism - and how to trace live gene expression during embryogenesis using the Endrov microscopy framework.(C. elegans), May 16 - Thomas Bürglin, Karolinska Institute, Huddinge (Invited speaker)
    Abstract: In the first part of the talk I will give an overview of the C. elegans model system, its lineage and development. In the second part of the talk, I will show how we can use the new microscopy framework Endrov to record 4D gene expression live during embryogenesis to examine transcription factors involved in cell fate decisions. Such data should provide a basis for developmental systems biology.
    Some references: www.wormbook.org, www.wormatlas.org, www.wormbase.org and Hench, J., Henriksson, J., Lüppert, M., and Bürglin, T.R. (2009). Spatio-temporal reference model of Caenorhabditis elegans embryogenesis with cell contact maps. Dev Biol 333, 1-13. - www.endrov.net
  • 7. Organism morphology and 3D-modeling (3D-modeling of cells and cell populations), May 23 - Lena Klasén
    Abstract: In this seminar I will give a very brief overview of organism modeling and analysis from an imaging point-of-view. The understanding of biological processes such as the development of body shape and organization using biomedical imaging techniques will be discussed, pinpointing some topics in the cross section of the scientific disciplines involved.

Informationsansvarig: Martin D. Mileros
Senast uppdaterad: 2012-05-30