Multivesicular Assemblies as Real-World Testbeds for Embryogenic Evolutionary Systems

Embryogenic evolution emulates in silico cell-like entities to get more powerful methods for complex evolutionary tasks. As simulations have to abstract from the biological model, implicit information hidden in its physics is lost. Here, we propose to use cell-like entities as a real-world in vitro testbed. In analogy to evolutionary robotics, where solutions evolved in simulations may be tested in real-world on macroscale, the proposed vesicular testbed would do the same for the embryogenic evolutionary tasks on mesoscale. As a first step towards a vesicular testbed emulating growth, cell division, and cell differentiation, we present a modified vesicle production method, providing custom-tailored chemical cargo, and present a novel self-assembly procedure to provide vesicle aggregates of programmable composition.

[1]  J. Crocker,et al.  Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  E. Ruppin Evolutionary autonomous agents: A neuroscience perspective , 2002, Nature Reviews Neuroscience.

[3]  Jianbin Huang,et al.  Transition between Higher-Level Self-Assemblies of Ligand−Lipid Vesicles Induced by Cu2+ Ion , 2003 .

[4]  Tughrul Arslan,et al.  2003 NASA/DoD Conference on Evolvable Hardware , 2002, NASA/DoD Conference on Evolvable Hardware, 2003. Proceedings..

[5]  Joyce Y Wong,et al.  Patterning adjacent supported lipid bilayers of desired composition to investigate receptor-ligand binding under shear flow. , 2004, Langmuir : the ACS journal of surfaces and colloids.

[6]  J. Weaver,et al.  Theory of electroporation: A review , 1996 .

[7]  J. Storhoff,et al.  A DNA-based method for rationally assembling nanoparticles into macroscopic materials , 1996, Nature.

[8]  Ingo Rechenberg,et al.  Evolutionsstrategie '94 , 1994, Werkstatt Bionik und Evolutionstechnik.

[9]  J. Miller,et al.  Guidelines: From artificial evolution to computational evolution: a research agenda , 2006, Nature Reviews Genetics.

[10]  E. Grell,et al.  Carriers and specificity in membranes. IV. Model vesicles and membranes. The formation of asymmetrical spherical lecithin vesicles. , 1971, Neurosciences Research Program bulletin.

[11]  S. Singer,et al.  The Fluid Mosaic Model of the Structure of Cell Membranes , 1972, Science.

[12]  S. Boxer,et al.  Effects of linker sequences on vesicle fusion mediated by lipid-anchored DNA oligonucleotides , 2009, Proceedings of the National Academy of Sciences.

[13]  Risto Miikkulainen,et al.  A Taxonomy for Artificial Embryogeny , 2003, Artificial Life.

[14]  Alexei V Tkachenko,et al.  Errorproof programmable self-assembly of DNA-nanoparticle clusters. , 2006, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  Valeria T Milam,et al.  DNA-mediated phase behavior of microsphere suspensions. , 2007, Langmuir : the ACS journal of surfaces and colloids.

[16]  J. Crocker,et al.  Colloidal interactions and self-assembly using DNA hybridization. , 2005, Physical review letters.

[17]  S. Boxer,et al.  Arrays of mobile tethered vesicles on supported lipid bilayers. , 2003, Journal of the American Chemical Society.

[18]  Raphael Zahn,et al.  DNA-induced programmable fusion of phospholipid vesicles. , 2007, Journal of the American Chemical Society.

[19]  J. Rothman,et al.  Energetics and dynamics of SNAREpin folding across lipid bilayers , 2007, Nature Structural &Molecular Biology.

[20]  J. Benkoski,et al.  Lateral mobility of tethered vesicle-DNA assemblies. , 2005, The journal of physical chemistry. B.

[21]  Vincent Noireaux,et al.  A vesicle bioreactor as a step toward an artificial cell assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Vladimir Torchilin,et al.  Multifunctional and stimuli-sensitive pharmaceutical nanocarriers. , 2009, European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V.

[23]  D Needham,et al.  Avidin-biotin interactions at vesicle surfaces: adsorption and binding, cross-bridge formation, and lateral interactions. , 1996, Biophysical journal.

[24]  Oleg Gang,et al.  Stepwise surface encoding for high-throughput assembly of nanoclusters. , 2009, Nature materials.

[25]  Vivek M Prabhu,et al.  Nanoparticle assembly: DNA provides control. , 2009, Nature materials.

[26]  Julian Francis Miller,et al.  Evolution in materio: looking beyond the silicon box , 2002, Proceedings 2002 NASA/DoD Conference on Evolvable Hardware.

[27]  Horst Vogel,et al.  An integrated self-assembled nanofluidic system for controlled biological chemistries. , 2008, Angewandte Chemie.

[28]  Green Nm,et al.  Avidin and streptavidin. , 1990 .

[29]  S. Singer,et al.  The fluid mosaic model of the structure of cell membranes. , 1972, Science.

[30]  Pierre-Alain Monnard,et al.  Preparation of vesicles from nonphospholipid amphiphiles. , 2003, Methods in enzymology.

[31]  Peter J. Bentley,et al.  Three Ways to Grow Designs: A Comparison of Evolved Embryogenies for a Design Problem , 1999 .

[32]  T. Vanderlick,et al.  Specific binding of different vesicle populations by the hybridization of membrane-anchored DNA. , 2007, The journal of physical chemistry. A.

[33]  Sophie Pautot,et al.  Engineering asymmetric vesicles , 2003, Proceedings of the National Academy of Sciences of the United States of America.