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Gene Silencing

Gene Silencing. Bob Anderssen CSIRO Mathematical and Information Sciences Peter Waterhouse CSIRO Plant Industry Thanks to various CMIS and CPI colleagues. Contents. What is Gene Silencing? The Natural Mechanism: Virus Control and Developmental Control

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Gene Silencing

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  1. Gene Silencing Bob Anderssen CSIRO Mathematical and Information Sciences Peter Waterhouse CSIRO Plant Industry Thanks to various CMIS and CPI colleagues.

  2. Contents • What is Gene Silencing? • The Natural Mechanism: Virus Control and Developmental Control (An “Emergence” Complex System Science Phenomenon) • Scientific Exploitation: Knockouts and Knockdowns • The Basic Ordinary Differential Equation Model • Easy to write down complex models and solve (Maple) • Mathematical Experimentation utilizing Plant Breeding Data • Opportunities • New mutants using knockouts. • Designing knockout strategies (Combinatorial Optimization – CMIS) • Designing new plant architecture. • How can Complex System Science assist?

  3. dsRNA mediated gene silencing Dicers Argonautes Bind mRNA Cleavage

  4. Opportunities for CSS AG04 24nt dsRNA templates DCL3 DCL2 DCL4 DCL1 22nt 21nt 21nt siRNA miRNA siRNA AG0 AG0 AG01 mRNA cleavage Virus RNA cleavage mRNA cleavage Developmental regulation Viral defence

  5. Viral Control (left hand side)

  6. AAAAAAA 1 2 AAAAAAA- RNAi mechanism – Mimicking Viral Control mRNA dsRNA

  7. c AAAAAAA M 2 1 3 AAAAAAA- RNAi mechanism cD mRNA dsRNA cS AAAAAAA- siRNA

  8. AAAAAAA AAAAAAA 4 AAAAAAA- RNAi mechanism mRNA dsRNA AAAAAAA- siRNA

  9. AAAAAAA AAAAAAA AAAAAAA- 5 RNAi mechanism mRNA dsRNA AAAAAAA- siRNA

  10. The Basic Ordinary Differential Equation Model

  11. Maple:Mathematical Experimentation – Steady State Ranking

  12. The Opportunity • Gene Knockout: Introduce dsRNA as hairpin RNA (hpRNA) to silence some specific gene. • Trick the plant in to shutting down or re-routing specific molecular pathways to alter biological activities. e.g. - flowering time - leaf shape - yield index - oil quality

  13. Col Dcl2 Dcl4 Dcl2,Dcl4 Dcl2,Dcl3Dcl4

  14. Synthetic miRNAs CUC1/2 syn miRNA Wt CUC1/2 syn miRNA

  15. How can CSS assist? • Designing Knock/Knockdown Strategies (combinatorial optimization – CMIS) • Assist with the Biological and Mathematical Challenges as they Unfold.

  16. AG0 AG0 AG01 Gene Silencing Pathways in Plants Heterochromatin formation AG04 24nt dsRNA templates RDR6 DCL3 DCL2 DCL4 DCL1 22nt 21nt 21nt miRNA siRNA ta-siRNA mRNA cleavage Virus RNA cleavage mRNA cleavage Control of developmental timing Developmental regulation Viral defence

  17. Ciliates Insects 975 1967 Mammals 1550 Fungi Green Algae 1625 + Rice 55 + Maize 955 <5 15 60 Monocots + Wheat 70 10 200 Barley + 270 Non-plant dicer Poplar dcl1 dcl1 90 10 Dicots dcl2a dcl2a Arabidopsis dcl2b dcl2b 165 dcl3a dcl3a 25 dcl3b dcl3b dcl4 dcl4 Evolutionary tree of dicer genes in plants Giardia 2,300 Large scale gene duplication Time in million years (My)

  18. Gene Silencing Pathways in Arabidopsis(Choose an appropriate Biological Model System) 2 3 1 4 1

  19. Thank you for your attention! • What is Gene Silencing? • The Natural Mechanism: Virus Control and Developmental Control (An “Emergence” Complex System Science Phenomenon) • Scientific Exploitation: Knockouts and Knockdowns • The Basic Ordinary Differential Equation Model • Easy to write down complex models and solve (Maple) • Mathematical Experimentation utilizing Plant Breeding Data • Opportunities • New mutants using knockouts. • Designing knockout strategies (Combinatorial Optimization – CMIS) • Designing new plant architecture. • How can Complex System Science assist?

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