1 / 22

Algorithmic systems biology propels nutrigenomics

Algorithmic systems biology propels nutrigenomics. Marco Scotti. Centre for Computational and Systems Biology The Microsoft Research - University of Trento. September 16th, 2010. Scotti - Roma, September 16th, 2010. Overview. Nutrigenomics and personalized diet

adamma
Télécharger la présentation

Algorithmic systems biology propels nutrigenomics

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Algorithmic systems biology propels nutrigenomics Marco Scotti Centre for Computational and Systems BiologyThe Microsoft Research - University of Trento September 16th, 2010 Scotti - Roma, September 16th, 2010

  2. Overview • Nutrigenomics and personalized diet • Algorithmic systems biology in nutrigenomics • Sustainable health: nutrigenomics and environment • Ecological networks to predict risks of secondary extinctions • Simulations and network analysis for dealing with a multi-scale approach Scotti - Roma, September 16th, 2010

  3. What is nutrigenomics? Scotti - Roma, September 16th, 2010

  4. DNA methylation, cancer and nutrients • DNA methylation is an effective suppressor of gene expression • Changes in methylation patterns may contribute to the development of cancer • Dietary factors that are involved in folate cycle provide the most compelling data for the interaction of nutrients and DNA methylation • Micronutrients that influence the supply of methyl groups are folate (vitamin B9), vitamin B12, vitamin B6, methionine, chlorine, selenium and alcohol Scotti - Roma, September 16th, 2010

  5. Folate cycle and cancer Davis, CD & Uthus, EO. Exp. Biol. Med. 229, 988-995 (2004) Scotti - Roma, September 16th, 2010

  6. Folate and cancer prevention Folate (vitamin B9) is thought to play a significant role in cancer prevention • Folate deficiency: • Decreases intracellular S-adenosylmethionine (SAM) which inhibits cytosine methylation in DNA • Activates proto-oncogenes • Induces malignant transformations • Causes DNA precursor imbalances • Misincorporates uracil into DNA • Promotes chromosome breakage Scotti - Roma, September 16th, 2010

  7. Folate and ethanol Mason, JB & Choi, SW. Alcohol 35, 235-241 (2005) Scotti - Roma, September 16th, 2010

  8. Folate and cancer risk: timing and dose Although increases in folate before the existence of preneoplastic lesions (such as aberrant crypt foci or polyps in the colon) can prevent tumor development, supplementation with synthetic folic acid may enhance progression once preneoplastic lesions are present Ulrich, CM. Am. J. Clin. Nutr. 86, 271-273 (2007) Scotti - Roma, September 16th, 2010

  9. Folate and MTHFR C677T polymorphism MTHFR polymorphism affects the distribution between folate species (green) used for DNA and RNA syntheses, or protein synthesis Ueland, PM et al. Trends in Pharmacological Sciences 22, 195-201 (2001) Scotti - Roma, September 16th, 2010

  10. Nutrition and sustainability POLLINATOR (fitness) CROP (apple) HUMAN (health) Scotti - Roma, September 16th, 2010

  11. Healthy and sustainable diets A – B – C – D D – B – C – A A B Environmental sustainability C D Human health Scotti - Roma, September 16th, 2010

  12. Food in agro-ecosystems Specialist parasitoid HIPV VP Generalist predator Herbivore James, DG & Grasswitz, TR. BioControl 50, 871-880 (2005) Scotti - Roma, September 16th, 2010

  13. Ecological networks Food webs are schematic representations of who eats whom in ecosystems Plant-ant Host-parasite Plant-pollinator Plant-seed disperser Scotti - Roma, September 16th, 2010

  14. Rooted food webs • The energy that sustains ecosystems comes from outside the system (i.e., solar radiation) • We can connect every primary producer with this "Root" node • Mapping the extent of secondary extinctions is equivalent to measuring how many nodes will be disconnected from the “Root” node, when an extinction occurs Scotti - Roma, September 16th, 2010

  15. Secondary extinctions As human activity threats the functioning of ecological systems (by habitat destruction, fragmentation, possibly causing climate change and invasions) we face the problem of how to understand and hopefully manage primary and secondary extinctions Scotti - Roma, September 16th, 2010

  16. Dominator tree Dominator tree unfolds the complex food web architecture, yielding a simpler topology made of linear pathways that are essential for energy delivery Food web Dominator tree Scotti - Roma, September 16th, 2010

  17. Ythan Estuary The Ythan Estuary is the tidal component of the Ythan River, emptying into the North Sea approximately 19 kilometres north of Aberdeen, Scotland Food web Dominator tree Scotti - Roma, September 16th, 2010

  18. Error and attack sensitivity Error Sensitivity (ES) = the fraction of species that would go extinct following a random removal Attack sensitivity (AS) = it represents the maximum damage that we can make with a single node removal. AS ranges between 0 and 1 Scotti - Roma, September 16th, 2010

  19. Node centralities Where are the clusters and who is in them? Who is in the core of the network? Who are the connectors, generalists and specialists? Who is on the periphery? Degree Centrality Closeness Centrality Betweenness Centrality Scotti - Roma, September 16th, 2010

  20. Fragility in ecosystems Natural-ecosystem Agro-ecosystem Scotti - Roma, September 16th, 2010

  21. Local and global properties 0.4 Density 2 Diameter Centrality Subgraph Degree distribution Scotti - Roma, September 16th, 2010

  22. Algorithmic systems biology propels nutrigenomics Marco Scotti marcoscot@gmail.com Centre for Computational and Systems BiologyThe Microsoft Research - University of Trento September 16th, 2010 Scotti - Roma, September 16th, 2010

More Related