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Systems Biology Seminar Series


 

Wednesday 20th October 2010: Dr Philip Gerlee (Gothenburg and Chalmers Universities, Sweden)

Structural correlations in bacterial metabolic networks

Abstract

Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships. We consider the 'super-network' consisting of the union of all networks where each reaction-node is tagged with the number of organisms it belongs to (organism degree, OD). Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are much more likely to be connected to each other compared to a random null-model, and this trend persists up to a distance of five reactions, which is similar to the average pathway length of 4.4 reactions, as defined in MetaCyc. Further, we propose a neutral model of metabolic evolution driven by horizontal gene transfer (HGT), which is only directed by biochemical constraints. The model is intialised with a single reaction-node, and by adding new nodes one at time metabolic networks are formed. Although these networks are unrelated and their only similarity stems from biochemical constraints, their 'super-network' still exhibits the same structure as the bacterial counter-part. This suggests that bacterial metabolic network evolve through HGT and to a large extent are formed by biochemical constraints.

 

1pm in the MIB lecture theatre, followed by refreshments in the cafeteria area.



For further information, please contact Kieran Smallbone.

 

2010 Series

20th October Philip Gerlee (Gothenburg and Chalmers Universities, Sweden)
Structural correlations in bacterial metabolic networks
   
21st July Prof David Fell (School of Life Sciences, Oxford Brookes University)
Control of flux in the mammalian TCA cycle
   
9th June Prof Ion Petre (Abo Akademi University, Finland)
Control strategies for the regulation of the eukaryotic heat shock response
   
12th May Prof Murray Grant (School of Biosciences, University of Exeter)
Suppression of plant defense responses by bacterial phytopathogens - Global insights into the role of plant hormones
   
31st March Dr Svetlana Amirova (University of Leicester)
Uncovering the design principles of polyamine regulation in yeast: An integrated modelling and experimental study


2009 Series

25th November Prof Denis Noble (Oxford Cardiac Electrophysiology Group - OCEG)
On The Music of Life: A new paradigm for biology (pdf)
   
25th November Dr Thierry Le Bihan (Centre for Systems Biology at Edinburgh - CSBE)
From 15N metabolic labelling to targeted LC-MS: Different strategies applied to Systems Biology (pdf)
   
28th October Prof Béla Novák (Oxford Centre for Integrative Systems Biology - OCISB)
(Ir)reversible decisions in dynamic cell biology and how they work
   
15th July Dr Christoph Sensen (The Sun Center of Excellence for Visual Genomics)
From 2D Bioinformatics to 4D Systems Biology
   
20th May Dr Declan Bates (Department of Engineering, University of Leicester)
A control engineering analysis of cAMP signalling networks in aggregating dictyostelium cells
   
29th April Dr Nick Monk (School of Mathematical Sciences, University of Nottingham)
Delay-driven oscillations in the notch signalling network
   
17th March Prof Michael White (University of Liverpool)
Spatial and temporal information encoding by the NF-κB system


2008 Series

10th September Dr Mark Roberts (University of Oxford)
Determining signal pathway connectivity using control engineering tools (abstract)
   
9th July Prof Jack Pronk (The Kluyver Centre)
Regulation and evolutionary adaptation of glycolytic capacity in Saccharomyces cerevisiae
   
14th May Dr Adriano Henney (AstraZeneca)
Challenges and opportunities for drug discovery and systems biology: A perspective (pdf)
   
9th April Dr Markus Kollmann (Humboldt University, Berlin)
Perfect Robustness against Non-Genetic Variations in Bacterial Signaling (abstract)


2007 Series

12th December Prof Andrew Millar (University of Edinburgh)
Biological timing for days and for years (pdf)
   
28th November Dr Andrzej Kierzek (University of Surrey)
The interplay between gene regulatory and metabolic reaction networks (pdf)
   
8th August Dr Ana Martins (Virginia Tech)
Beyond the Yap1p regulon in the Saccharomyces cerevisiae response to oxidative stress (abstract)
   
20th June Prof Pedro Mendes (University of Manchester)
Numerical biology: Uses of in silico biochemical networks (pdf)
   
9th May Prof Muffy Calder (University of Glasgow)
Modelling biochemical signalling pathways: Computing science meets the life sciences (pdf)
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