Metabolic networks

1
Metabolic networks

• Analyses and prediction of metabolic networks
  based on genetically modified organisms with gene
  specific knock-outs or genetically controlled
  modifications of primary and secondary
  metabolism
• Primary metabolism - biochemical pathways that
  are in general common to all cells
• Secondary metabolism - specialised pathways,
  often involved in defence
• Postdoc in bioinformatics/metabolic networks
• Start January 2004
• Finn Drabløs, Sigurd Skogestad, Bjørn K. Alsberg,
  Mette Langaas, Svein Valla, Atle M. Bones

2
Networks everywhere ...

• Regulatory and signalling networks
• Event ? signal ? process
• Trp ? Trp repressor ? Blocks Trp operon
  transcription
• Metabolic networks
• Substrate ? substrate ? substrate ? product
• citrate ? isocitrate ? ?-ketoglutarate ? succinyl
  CoA ? succinate
• Interaction networks
• A B ? AB
• Cytochrome subunit L M H ? photosynthetic
  reaction centre
• Networks overlap and interact
• Systems biology

3
Research project

• Understand how processes are organised into
  networks, and how networks can be manipulated
  (metabolic engineering)
• Raw data from postdoc in biotechnology and other
  sources
• Transcriptional profiling on up to 52.000 unique
  genes
• LC-MS, GC-MS, HPLC
• NMR
• Integration with other data sources
• KEGG, LIGAND, Global Pathways DB, MDDB, Transfac,
  BIND,
• Classification
• Gene expression data
• Effect/response data
• Metabolic modelling (the in silico cell)

4
Programme for bioinformatics

• Inter-faculty collaboration to co-ordinate
  bioinformatics at NTNU
• DMF - Faculty of Medicine
• NT - Faculty of Natural Sciences and Technology
• IME - Faculty of Engineering Science and
  Technology
• Programme committee
• Kjell Bratbergsengen (committee leader), Finn
  Drabløs (general leader), Arne Halaas, Atle
  Bones, Catharina Davies, Mette Langaas, Astrid
  Lægreid, Bjørn Alsberg, Erik Must (Fondsfinans),
  Per Magnus (Nasjonalt folkehelseinstitutt),
  Birgit Hafeld Borgen (co-ordinator w/FUGE,
  temporary appointment)
• Mandate (excerpt) The main task for the
  committee will be to co-ordinate and stimulate
  the inter-faculty activity in bioinformatics at
  NTNU. Focus will be on education and research

5
Programme for bioinformatics

• Supported by
• NTNU Strategi omstilling
• Bioemit
• IME DMF
• Tools
• Professor in bioinformatics
• Svanhild og Arne Musts fond for medisinsk
  forskning, DMF
• Network for bioinformatics
• Co-ordinate education
• Co-ordinate applications
• Meetings and seminars
• Marketing of bioinformatics