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Quantitative symbiogenesis

Explore the application of DEB theory to symbiogenesis within various levels of biological organization, with implications for ecotoxicology and biotechnology. Learn about product formation, nutrient limitation, and symbiotic relationships. Download the DEBtool for free.

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Quantitative symbiogenesis

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  1. Quantitative symbiogenesis Van Gogh NWO-exchange programme F-NL on aggregation methods & time scale separation Kooijman, Bas, VU-Amsterdam Kooi, Bob, VU-Amsterdam Auger, Pierre, Claude-Bernard Univ.-Lyon Poggiale, Jean-Christophe, Centre d’Oceanol. -Marseilles Dept of Theoretical Biology Vrije Universiteit, Amsterdam http://www.bio.vu.nl/thb/

  2. Contents of lecture Internat Conf on Mathematics and Biology of the SMB Knoxville, 2002/07/13-16 • symbiosis in context of DEB research • elements of simplest DEB model • symbiosis in context of evolution • application of DEB theory to symbiogenesis • results

  3. Dynamic Energy Budget theory • for metabolic organisation of all life on earth • first principles • quantitative • Biological equivalent of Theoretical Physics • Primary target: the individual with consequences for • sub-organismal organization • supra-organismal organization • Relationships between levels of organisation • Applications in • ecotoxicology • biotechnology • Direct link with empiry

  4. DEB-ontogeny-IBM

  5. DEB-ontogeny-IBM Tom Hallam visits Delft 1985/08/12

  6. Reserve dynamics • Increase: assimilation  surface area • Decrease: catabolism  reserve/structure • First order process on the basis of densities follows from • weak homeostatis of biomass = structure + reserve • partitionability of reserve dynamics • Mechanism: structural homeostasis • key feature: avoiding dilution by growth

  7. Product Formation According to Dynamic Energy Budget theory: Product formation rate = wA. Assimilation rate + wM. Maintenance rate + wG . Growth rate For pyruvate: wG<0 ethanol pyruvate,m g/l glycerol, ethanol, g/l pyruvate glycerol throughput rate, 1/h Glucose-limited growth of Saccharomyces

  8. 1 Reserve – 1 Structure

  9. 2 Reserves – 1 Structure

  10. Simultaneous Substrate Processing Flux of C: Chemical reaction: 1A + 1B 1C Poisson arrival events for molecules A and B Standard enzyme kinetics: Substrate Conc. product flux (MM-kinetics) Synthesizing Unit-concept: irreversible SU-substrate binding Substrate conc substrate flux (transport module) Substrate flux product flux + rejected substrate flux

  11. Simultaneous Nutrient Limitation B12 content, 10-21 mol/cell P content, fmol/cell Specific growth rate of Pavlova lutheri as function of intracellular phosphorus and vitamin B12 at 20 ºC Data from Droop 1974 Note the absence of high contents for both compounds due to damming up of reserves, and low contents in structure (at zero growth)

  12. Reserve Capacity & Growth low turnover rate: large reserve capacity high turnover rate: small reserve capacity DEBtool is freely downloadable from http://www.bio.vu.nl/thb/deb/

  13. Organism substrate product An organism converts substrates into products and a bit more of itself

  14. Symbiosis substrate substrate Major basis: exchange of products between partners: syntrophy with transitions to competition & parasitism & predation Mutualism: not essential “beneficial” involves an optimization criterion

  15. Greenanimals Dicranophorus caudatus Encentrum saundersiae Chlorohydra viridissima Itura aurita Rotifera corals Typhloplana viridata Dalyellia viridis Cnidaria Platyhelminthes From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, Stuttgart

  16. Green fungi: lichenes From: Nash, T. H. 1996 Lichen biology, Cambridge UP

  17. Greenciliates Ophrydium versatile Strongylidium crassum Strombidium viride Urostyla viridis Stentor polymorphus Didinium faurei Teuthophrys trisulcata Paramecium bursaria Spathidium opimum Prorodon viridis From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, Stuttgart

  18. Greenprotists Heterophrys myriepoda Raphidiophrys viridis Acanthocystis mimetica Heliozoa From: Streble, H. & Krauter, D. 1973 Das Leben im Wassertropfen. Komos, Stuttgart Wolf-Gladrow, D. A., Bijma, J. & Zeebe, R. E.1999 Mar. Chem 64: 181-198 Foraminifera Globigerinoides sacculifer

  19. Choroplast evolution Delwiche, C. F. 1999. Tracing the thread of plastid diversity through the tapestry of life. Am. Nat. 154, S164-S177

  20. http://www.bio.vu.nl/thb/ “education”,”cycles” many life cycle pictures Survey of Organisms Basidiomycota Eustigmatophyceae Ascomycota Raphidophyceae Zygomycota brown algae Phaeophyceae Xanthophyceae Plasmodiophoromycota Microsporidia Chlorarachnida Chytridiomycota Cercomonada Labyrinthulomycota Chrysophyceae Bicosoecia animals Synurophyceae Percolozoa Pseudofungi Neomonada Euglenozoa Dictyochophyceae Opalinata Dinozoa Kinetoplastida Pelagophyceae Sporozoa Diplonemida diatoms Bacillariophyceae Ciliophora Myxomycota plants Cormophyta Protostelida Prymnesiophyceae Cryptophyceae Rhizopoda green algae Chlorophyceae Archaeprotista Glaucophyceae Actinopoda Bacteria red algae Rhodophyceae Xenophyophora Trichozoa Granuloreticulata Metamonada

  21. Steps in symbiogenesis Internalization Free-living, clustering Free-living, homogeneous Reserves merge Structures merge

  22. Steps in symbiogenesis in the context of the DEB theory • 2 populations, substrates, products • from substitutable to complementary products • spatial clustering • internalization • weak homeostasis for structure • from concentrations to fluxes of internal prod. • strong homeostasis for structure • coupling of assimilation fluxes • coupling of reserve dynamics • weak homeostasis for reserves • strong homeostasis for reserves

  23. Chemostat Steady States Free living Products complementary Endosymbiosis Exchange on conc-basis Free living Products substitutable biomass density Exchange on flux-basis Structures merged Reserves merged Host uses 2 substrates throughput rate symbiont host

  24. Results It is possible to merge partners smoothly through incremental changes of parameter values Homeostasis can be achieved gradually range of ratio of structures reduces Partitionability argument for reserve kinetics can be reformulated in a mergebility argument If partners follow DEB rules, symbiogenesis can be such that symbiosis again follows DEB rules We made some progress in understanding the modular organization of cell’s metabolism in an evolutionary context

  25. Thank you for your attention Free internet course on DEB theory February-April 2003 (part time) http://www.bio.vu.nl/thb/deb/course/ Tom: congratulations !

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