Abstract

In the frame of several European projects (e.g., HYDRA, ADAPT and ROBOTCUB), we pioneered in biologically relevant computer science not only by a renunciation of the one-to-one mapping from genotype to phenotype, but also by introducing embryogenic development processes exploiting simulated physics. Based on simulated genetic regulatory networks for ontogenetic development, gradients of signaling molecules, interactions of genes, morphogenes, and cell physics we successfully applied cellular mechanisms (cell adhesion, migration, death, differentiation, and induction) to the control of modular robots consisting of hundreds of basic modules in silico [1]. Whilst CPU-intensity of physics simulation was conceivable, the lack of a simple real-world testbed to validate in silico results thereby became obvious. In order to bridge this gap, we implemented the first artificial multicompartment wetware system of programmable composition and spatial arrangement [2] and discussed its potential applications in validation of in silico results [3], personalized healthcare [4, 5], and antiviral drug design [6]. Moreover, new laboratory protocols that increase compartment handling and manageability, new preparation techniques that internally define and structure the lumen of the compartments were implemented.

Keywords: Embryogenic evolution, wetware, self-assembly, programmable architecture, real-world testbed, personalized healthcare, antiviral drug design.

Project Leadership and Contacts: Dr. Peter Eggenberger (Project Leader), Maik Hadorn

Funding Source: Swiss National Science Foundation: Independent Basic Research

Project Number: 200020-118127

Duration of Project: Oct 2005 to Sep 2009

Background

Current strategies in the design of human-made hardware artifacts mostly rely on fixed-morphology robots integral in architecture and task. The ambitious attempt to anticipate and control every detail of an artifact is expressed not only in masterpieces of human engineering such as electronic computers and industrial robots but more recently also in synthetic biology and nanorobotics. These ‘classical’ design principles may reach limits as the task becomes too complex and/or unpredictable. Hence the modular design of multicellular organism provides inspiration to tackle these shortcomings. By implementing the principle of ‘a task shared is a task halved’ the use of pre-existing units that solve the task as a compound of n entities not only reduces the complexity of the single units but provides the potential to create new topologies to accomplish a task by self-reconfiguration. Decentralized local control strategies accompany the modular design of self-reconfigurable robots complementing the cerebralisation as prevalent architectural and control concept of integral robots. By entrusting competence to the single modules the entire systems becomes more robust and adaptive [7]. Direct encoding schemes, wherein each primitive of the phenotype is represented by a single genetic parameter, no longer work for complex tasks. In nature, there is no exact representation of the body plan in the genome. Morphology is rather a result of manifold interactions of genetic, epigenetic and environmental factors. Thereby, the genome codes for shifts in the equilibrium of physical-chemical processes; whilst the implementation of the processes is outsourced to inherent material properties [8].

By getting inspired by nature, man-made technologies changed over the last two decades accounting for these insights provided by natural sciences. The shift in paradigm is represented by a deflection of interest from integral hardware systems that are centrally controlled and that are built of linear materials to multicompartment wetware systems composed of biologically relevant media. The conception of the Embryogenic Evolution System (EES) projects reflects this shift of scientific focus. In order to further evaluate biologically inspired control strategies assessed to be of key importance in the European project HYDRA, the EES project based on multi-modular design, localized control, and exploitation of the medium. In the process of implementation, the necessity of miniaturization to the microscopic scale and the usage of biologically relevant media became obvious.

Microscopic compartments built of organic lipid molecules have gained importance in distinct fields of research. Recently, wet laboratory approaches that aim to engineer artificial living systems from nonliving substances were designated as ‘Living Technology’; a technology that is based on the powerful core features of life [9]. Current systems applying artificial cell-like compartments represent high-end products in Life sciences or Living Technology. Although offering a division of different membrane functions and reaction containers, the few representatives of superstructures composed of n entities are restricted to bioreactors [10-12], cosmetic applications [13], although they were proposed as multicomponent or multifunctional drug delivery systems long ago [14-17]. By introducing internal organelle-like compartments, the systems of Bolinger [12] and Zasadzinski [14] bear even more analogies to eukaryotic cells than ‘simple’ assemblies of compartments [18]. The underrepresentation of multicompartment entities either individually operating or internally structuring bigger compartments is not due to a lack of interest, neither in replication of compartments nor in the programmable self-assembly of (multilammelar) multicompartment structures, but in shortcomings of the prevalent experimental protocols. In particular, protocols implementing replication of compartments depend on mechanical stress either induced by extrusion or shear forces [19, 20] and prevalent tethering mechanisms are either not reliable or lack more than two distinct classes of linkers. Hence asymmetric cell division, cell migration, and cell differentiation had to be emulated by self-assembled multicompartment aggregates of predefined architecture composed of n populations of compartments distinct in membrane and/or internal fluid composition.

Results and Relevance

The EES project may influence future research both in a technical and more conceptual way. The new protocol for in vitro vesicle preparation and modification ease procedural manageability. Microtiter plates and independent composition control of the intra- and intervesicular fluid enabling vesicle pelletization may complement the more challenging vesicle preparation of Pautot, Frisken and Weitz, whereby single tubes are used and a flow of medium has to be induced manually that detaches the vesicles from the interface between oil and hosting medium [21]. Modifications of the vesicle preparation protocol enabled the implementation of both high-throughput analyses [4, 6] and a new methodology to prepare internally compartmentalized vesicles [5]. The linkage process realized here that bases on hybridization of biotinylated ssDNA anchored to the vesicular surface via streptavidin and phospholipid-grafted biotinylated PEG tethers not only merges programmability, specificity and high degrees of complexity [22] of DNA with the strongest noncovalent biological interaction known [23], an extensive range of possible vesicle modifications, component modularity and availability off the shelf of streptavidin but the long and flexible phospholipid-grafted biotinylated PEG tethers provide mobility [24], high detachment resistance [25] and no intermembrane transfer of linkers [26, 27]. By doping vesicles with biotinylated PEG tethers universal anchor sites were introduced, which allow for constancy in the vesicle preparation protocol. As a consequence, there was no need to adapt vesicle preparation in dependence of different vesicle decorations. Moreover, the mobility of linkers inherent to lipid membranes was exploited to self-terminate the assembly process by an accumulation of linkers at the contact site [2].

Acknowledgments

References

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