Artificial cells: prospects for biotechnology

Modeling a minimal cell

One important aim of synthetic biology is to develop a self-replicating biological system capable of performing useful tasks. A mathematical model of a synthetic organism would greatly enhance its value by providing a platform in which proposed modifications to the system could be rapidly prototyped and tested. Such a platform would allow the explicit connection of genomic sequence information to physiological predictions. As an initial step toward this aim, a minimal cell model (MCM) has been formulated. The MCM is defined as a model of a hypothetical cell with the minimum number of genes necessary to grow and divide in an optimally supportive culture environment. It is chemically detailed in terms of genes and gene products, as well as physiologically complete in terms of bacterial cell processes (e.g., DNA replication and cell division). A mathematical framework originally developed for modeling Escherichia coli has been used to build the platform MCM. A MCM with 241 product-coding genes (those which produce protein or stable RNA products) is presented. This gene set is genomically complete in that it codes for all the functions that a minimal chemoheterotrophic bacterium would require for sustained growth and division. With this model, the hypotheses behind a minimal gene set can be tested using a chemically detailed, dynamic, whole-cell modeling approach. Furthermore, the MCM can simulate the behavior of a whole cell that depends on the cell's (1) metabolic rates and chemical state, (2) genome in terms of expression of various genes, (3) environment both in terms of direct nutrient starvation and competitive inhibition leading to starvation, and (4) genomic sequence in terms of the chromosomal locations of genes.

Stable, biocompatible lipid vesicle generation by solvent extraction-based droplet microfluidics

In this paper, we present a microfluidic platform for the continuous generation of stable, monodisperse lipid vesicles 20-110 μm in diameter. Our approach utilizes a microfluidic flow-focusing droplet generation design to control the vesicle size by altering the system's fluid flow rates to generate vesicles with narrow size distribution. Double emulsions are first produced in consecutive flow-focusing channel geometries and lipid membranes are then formed through a controlled solvent extraction process. Since no strong solvents are used in the process, our method allows for the safe encapsulation and manipulation of an assortment of biological entities, including cells, proteins, and nucleic acids. The vesicles generated by this method are stable and have a shelf life of at least 3 months. Here, we demonstrate the cell-free in vitro synthesis of proteins within lipid vesicles as an initial step towards the development of an artificial cell.

Liposomes as lubricants: beyond drug delivery

In this paper we review recent work (Goldberg et al., 2011a,b) on a new use for phosphatidylcholine liposomes: as ultra-efficient boundary lubricants at up to the highest physiological pressures. Using a surface force balance, we have measured the normal and shear interactions as a function of surface separation between layers of hydrogenated soy phophatidylcholine (HSPC) small unilamellar vesicles (SUVs) adsorbed from dispersion, at both pure water and physiologically high salt concentrations of 0.15 M NaNO(3). Cryo-Scanning Electron Microscopy shows each surface to be coated by a close-packed HSPC-SUV layer with an over-layer of liposomes on top. The shear forces reveal strikingly low friction coefficients down to 2×10(-5) in pure water system or 6×10(-4) in the 150 mM salt system, up to contact pressures of at least 12 MPa (pure water) or 6 MPa (high salt), comparable with those in the major joints. This low friction is attributed to the hydration lubrication mechanism arising from rubbing of the highly hydrated phosphocholine-headgroup layers exposed at the outer surface of each liposome, and provides support for the conjecture that phospholipids may play a significant role in biological lubrication.

Interactions between adsorbed hydrogenated soy phosphatidylcholine (HSPC) vesicles at physiologically high pressures and salt concentrations

Using a surface force balance, we measured normal and shear interactions as a function of surface separation between layers of hydrogenated soy phosphatidylcholine (HSPC) small unilamellar vesicles (SUVs) adsorbed from dispersion at physiologically high salt concentrations (0.15 M NaNO₃). Cryo-scanning electron microscopy shows that each surface is coated by a close-packed HSPC-SUV layer with an overlayer of liposomes on top. A clear attractive interaction between the liposome layers is seen upon approach and separation, followed by a steric repulsion upon further compression. The shear forces reveal low friction coefficients (μ = 0.008-0.0006) up to contact pressures of at least 6 MPa, comparable to those observed in the major joints. The spread in μ-values may be qualitatively accounted for by different local liposome structure at different contact points, suggesting that the intrinsic friction of the HSPC-SUV layers at this salt concentration is closer to the lower limit (μ = ~0.0006). This low friction is attributed to the hydration lubrication mechanism arising from rubbing of the hydrated phosphocholine-headgroup layers exposed at the outer surface of each liposome, and provides support for the conjecture that phospholipids may play a significant role in biological lubrication.

Preparation and characterization of single-enzyme nanogels

Enzymes have been incorporated in nanostructures in order to provide robust catalysts for valuable reactions, particularly those performed under harsh and denaturing conditions. This chapter describes the encapsulation of enzymes in polyacrylamide nanogels by a two-step in situ polymerization process for preparing robust biocatalysts. The first step in this process is the generation of vinyl groups on the enzyme surface, while the second step involves in situ polymerization using acrylamide as the monomer. Encapsulation of the enzyme in the hydrophilic, porous, and flexible polyacrylamide gel of several nanometers thick would help to both give a significantly enhanced thermostability and prevent the removal of essential water by polar solvents. The hydrophilic flexible polymer shell also allows the protein structure to undergo necessary conformational transitions during the catalytic reaction and, at the same time, impose marginal mass transfer restrictions for the substrates entering across the polymer shell. The effectiveness of this method is demonstrated with horseradish peroxidase (HRP), carbonic anhydrase, and lipase. The impacts of such an encapsulation on the activity and stability of enzymes are also discussed.

Selfishness versus functional cooperation in a stochastic protocell model

How to design an "evolvable" artificial system capable to increase in complexity? Although Darwin's theory of evolution by natural selection obviously offers a firm foundation, little hope of success seems to be expected from the explanatory adequacy of modern evolutionary theory, which does a good job at explaining what has already happened but remains practically helpless at predicting what will occur. However, the study of the major transitions in evolution clearly suggests that increases in complexity have occurred on those occasions when the conflicting interests between competing individuals were partly subjugated. This immediately raises the issue about "levels of selection" in evolutionary biology, and the idea that multi-level selection scenarios are required for complexity to emerge. After analyzing the dynamical behaviour of competing replicators within compartments, we show here that a proliferation of differentiated catalysts and/or improvement of catalytic efficiency of ribozymes can potentially evolve in properly designed artificial cells where the strong internal competition between the different species of replicators is somewhat prevented (i.e., by choosing them with equal probability). Experimental evolution in these systems will likely stand as beautiful examples of artificial adaptive systems, and will provide new insights to understand possible evolutionary paths to the evolution of metabolic complexity.

Synthetic biology of minimal living cells: primitive cell models and semi-synthetic cells

This article summarizes a contribution presented at the ESF 2009 Synthetic Biology focused on the concept of the minimal requirement for life and on the issue of constructive (synthetic) approaches in biological research. The attempts to define minimal life within the framework of autopoietic theory are firstly described, and a short report on the development of autopoietic chemical systems based on fatty acid vesicles, which are relevant as primitive cell models is given. These studies can be used as a starting point for the construction of more complex systems, firstly being inspired by possible origins of life scenarioes (and therefore by considering primitive functions), then by considering an approach based on modern biomacromolecular-encoded functions. At this aim, semi-synthetic minimal cells are defined as those man-made vesicle-based systems that are composed of the minimal number of genes, proteins, biomolecules and which can be defined as living. Recent achievements on minimal sized semi-synthetic cells are then discussed, and the kind of information obtained is recognized as being distinctively derived by a constructive approach. Synthetic biology is therefore a fundamental tool for gaining basic knowledge about biosystems, and it should not be confined at all to the engineering side.

ENVIRONMENT: a computational platform to stochastically simulate reacting and self-reproducing lipid compartments

'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to study the time evolution of reaction networks in heterogeneous conditions, particularly when supramolecular lipid structures (micelles, vesicles, etc) coexist with aqueous domains. These conditions are of special relevance to understand the origins of cellular, self-reproducing compartments, in the context of prebiotic chemistry and evolution. We contrast our simulation results with real lab experiments, with the aim to bring together theoretical and experimental research on protocell and minimal artificial cell systems.

Synthetic cells and organelles: compartmentalization strategies

The recent development of RNA replicating protocells and capsules that enclose complex biosynthetic cascade reactions are encouraging signs that we are gradually getting better at mastering the complexity of biological systems. The road to truly cellular compartments is still very long, but concrete progress is being made. Compartmentalization is a crucial natural methodology to enable control over biological processes occurring within the living cell. In fact, compartmentalization has been considered by some theories to be instrumental in the creation of life. With the advancement of chemical biology, artificial compartments that can mimic the cell as a whole, or that can be regarded as cell organelles, have recently received much attention. The membrane between the inner and outer environment of the compartment has to meet specific requirements, such as semi-permeability, to allow communication and molecular transport over the border. The membrane can either be built from natural constituents or from synthetic polymers, introducing robustness to the capsule.

Development and fabrication of nanoporous silicon-based bioreactors within a microfluidic chip

Multi-scale lithography and cryogenic deep reactive ion etching techniques were used to create ensembles of nanoporous, picolitre volume, reaction vessels within a microfluidic system. The fabrication of these vessels is described and how this process can be used to tailor vessel porosity by controlling the width of slits that constitute the vessel pores is demonstrated. Control of pore size allows the containment of nucleic acids and enzymes that are the foundation of biochemical reaction systems, while allowing smaller reaction constituents to traverse the container membrane and continuously supply the reaction. In this work, a 5.4 kb DNA plasmid was retained within the reaction vessels and labeled under microfluidic control with ethidium bromide as an initial proof-of-principle. Subsequently, a coupled enzyme reaction, in which glucose oxidase (GOX) and horseradish peroxidase (HRP) were contained and fed with a substrate solution of glucose and Amplex Red to produce fluorescent resorufin, was carried out under microfluidic control and monitored using fluorescent microscopy. The fabrication techniques presented are broadly applicable and can be adapted to produce devices in which a variety of high aspect ratio, nanoporous silicon structures can be integrated within a microfluidic network. The devices shown here are amenable to being scaled in number and organized to implement more complex reaction systems for applications in sensing and actuation as well as fundamental studies of biological reaction systems.

Constructing partial models of cells

Understanding the origin of life requires knowledge not only of the origin of biological molecules such as amino acids, nucleotides and their polymers, but also the manner in which those molecules are integrated into the organized systems that characterize cellular life. In this article, we introduce a constructive approach to understand how biological molecules can be arranged to achieve a higher-order biological function: replication of genetic information.

Considerations for the design and construction of a synthetic platform cell for biotechnological applications

The design and construction of an artificial bacterial cell could revolutionize biotechnological processes and technologies. A functional platform cell that can be easily customized for a pre-defined task would be useful for applications from producing therapeutics to decontaminating waste streams. The platform cell must be robust and highly efficient. A biotechnological platform cell is related to the concept of a minimal cell, but several factors beyond those necessary for a minimal cell must be considered for a synthetic organism designed for biotechnological applications. Namely, a platform cell must exhibit robust cell reproduction, decreased genetic drift, a physically robust cell envelope, efficient and simplified transcription and translation controls, and predictable metabolic interactions. Achieving a biotechnological platform cell will benefit from insights acquired from a minimal cell, but an approach of minimizing an existing organism's genome may be a more practical experimental approach. Escherichia coli possess many of the desired characteristics of a platform cell and could serve as a useful model organism for the design and construction of a synthetic platform organism. In this article we review briefly the current state of research in this field and outline specific characteristics that will be important for a biotechnologically relevant synthetic cell that has a minimized genome and efficient regulatory structure.

Biosynthesis of proteins inside liposomes

Protein expression is the most complex metabolic reaction that has been encapsulated in liposomes, mainly as an intermediate step toward the synthesis of minimal semisynthetic cells. Although there are different experimental approaches to achieving the synthesis of proteins inside liposomes and it is therefore not possible to give a standard recipe, all methods follow a general strategy, which is briefly discussed. On this basis, we provide general indications for designing and realizing protein-expressing liposomes. Our approach for the green fluorescent protein expression inside 200-nm extruded vesicles is described in detail.

Synthetic organisms and living machines : Positioning the products of synthetic biology at the borderline between living and non-living matter

The difference between a non-living machine such as a vacuum cleaner and a living organism as a lion seems to be obvious. The two types of entities differ in their material consistence, their origin, their development and their purpose. This apparently clear-cut borderline has previously been challenged by fictitious ideas of “artificial organism” and “living machines” as well as by progress in technology and breeding. The emergence of novel technologies such as artificial life, nanobiotechnology and synthetic biology are definitely blurring the boundary between our understanding of living and non-living matter. This essay discusses where, at the borderline between living and non-living matter, we can position the future products of synthetic biology that belong to the two hybrid entities “synthetic organisms” and “living machines” and how the approaching realization of such hybrid entities affects our understanding of organisms and machines. For this purpose we focus on the description of three different types of synthetic biology products and the aims assigned to their realization: (1) synthetic minimal cells aimed at by protocell synthetic biology, (2) chassis organisms strived for by synthetic genomics and (3) genetically engineered machines produced by bioengineering. We argue that in the case of synthetic biology the purpose is more decisive for the categorization of a product as an organism or a machine than its origin and development. This has certain ethical implications because the definition of an entity as machine seems to allow bypassing the discussion about the assignment and evaluation of instrumental and intrinsic values, which can be raised in the case of organisms.

Polymer hydrogel capsules: en route toward synthetic cellular systems

Engineered synthetic cellular systems are expected to become a powerful biomedical platform for the development of next-generation therapeutic carrier vehicles. In this mini-review, we discuss the potential of polymer capsules derived by the layer-by-layer assembly as a platform system for the construction of artificial cells and organelles. We outline the characteristics of polymer capsules that make them unique for these applications, and we describe several successful examples of microencapsulated catalysis, including biologically relevant enzymatic reactions. We also provide examples of subcompartmentalized polymer capsules, which represent a major step toward the creation of synthetic cells.

The role of biomacromolecular crowding, ionic strength, and physicochemical gradients in the complexities of life's emergence

We have developed a general scenario of prebiotic physicochemical evolution during the Earth's Hadean eon and reviewed the relevant literature. We suggest that prebiotic chemical evolution started in microspaces with membranous walls, where external temperature and osmotic gradients were coupled to free-energy gradients of potential chemical reactions. The key feature of this scenario is the onset of an emergent evolutionary transition within the microspaces that is described by the model of complex vectorial chemistry. This transition occurs at average macromolecular crowding of 20 to 30% of the cell volume, when the ranges of action of stabilizing colloidal forces (screened electrostatic forces, hydration, and excluded volume forces) become commensurate. Under these conditions, the macromolecules divide the interior of microspaces into dynamically crowded macromolecular regions and topologically complementary electrolyte pools. Small ions and ionic metabolites are transported vectorially between the electrolyte pools and through the (semiconducting) electrolyte pathways of the crowded macromolecular regions from their high electrochemical potential (where they are biochemically produced) to their lower electrochemical potential (where they are consumed). We suggest a sequence of tentative transitions between major evolutionary periods during the Hadean eon as follows: (i) the early water world, (ii) the appearance of land masses, (iii) the pre-RNA world, (iv) the onset of complex vectorial chemistry, and (v) the RNA world and evolution toward Darwinian thresholds. We stress the importance of high ionic strength of the Hadean ocean (short Debye's lengths) and screened electrostatic interactions that enabled the onset of the vectorial structure of the cytoplasm and the possibility of life's emergence.

Stochastic simulation and analysis of biomolecular reaction networks

BACKGROUND

In recent years, several stochastic simulation algorithms have been developed to generate Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks. However, the effects of various stochastic simulation and data analysis conditions on the observed dynamics of complex biomolecular reaction networks have not received much attention. In order to investigate these issues, we employed a a software package developed in out group, called Biomolecular Network Simulator (BNS), to simulate and analyze the behavior of such systems. The behavior of a hypothetical two gene in vitro transcription-translation reaction network is investigated using the Gillespie exact stochastic algorithm to illustrate some of the factors that influence the analysis and interpretation of these data.

RESULTS

Specific issues affecting the analysis and interpretation of simulation data are investigated, including: (1) the effect of time interval on data presentation and time-weighted averaging of molecule numbers, (2) effect of time averaging interval on reaction rate analysis, (3) effect of number of simulations on precision of model predictions, and (4) implications of stochastic simulations on optimization procedures.

CONCLUSION

The two main factors affecting the analysis of stochastic simulations are: (1) the selection of time intervals to compute or average state variables and (2) the number of simulations generated to evaluate the system behavior.

Block-copolymer vesicles as nanoreactors for enzymatic reactions

The impact of the spatial confinement of polystyrene-block-poly(acrylic acid) (PS-b-PAA) block copolymer (BCP) vesicles on the reactivity of encapsulated bovine pancreas trypsin is studied. Enzymes, as well as small molecules, are encapsulated with loading efficiencies up to 30% in BCP vesicles with variable internal volumes between 0.014 aL (internal vesicle diameter, d(in) = 30 nm) and 8 aL (d(in) = 250 nm), obtained by manipulating the vesicle preparation conditions. The kinetics of the trypsin-catalyzed reaction of a fluorogenic substrate inside and outside the vesicles is quantitatively estimated using fluorescence spectroscopic analyses in conjunction with the use of NaNO(2) as selective quencher for non-encapsulated fluorophores. The values of the catalytic turnover number obtained for reactions in differently sized nanoscale reactors show a significant increase (up to approximately 5x) with decreasing BCP vesicle volume, while the values of the Michaelis-Menten constant decrease. The observed increase in enzyme efficiency by two orders of magnitude compared to bulk solution is attributed to an enhanced rate of enzyme-substrate and molecule-wall collisions inside the nanosized reactors, as predicted in the literature on the basis of Monte Carlo simulations.

Carbon nanotube based artificial water channel protein: membrane perturbation and water transportation

We functionalized double-walled carbon nanotubes (DWCNTs) as artificial water channel proteins. For the first time, molecular dynamics simulations show that the bilayer structure of DWCNTs is advantageous for carbon nanotube based transmembrane channels. The shielding of the amphiphilic outer layer could guarantee biocompatibility of the synthetic channel and protect the inner tube (functional part) from disturbance of the membrane environment. This novel design could promote more sophisticated nanobiodevices which could function in a bioenvironment with high biocompatibility.

Importance of translation-replication balance for efficient replication by the self-encoded replicase

In all living systems, the genetic information is replicated by the self-encoded replicase (Rep); this can be said to be a self-encoding system. Recently, we constructed a self-encoding system in liposomes as an artificial cell model, consisting of a reconstituted translation system and an RNA encoding the catalytic subunit of Qbeta Rep and the RNA was replicated by the self-encoded Rep produced by the translation reaction. In this system, both the ribosome (Rib) and Rep bind to the same RNA for translation and replication, respectively. Thus, there could be a dilemma: effective RNA replication requires high levels of Rep translation, but excessive translation in turn inhibits replication. Herein, we actually observed the competition between the Rib and Rep, and evaluated the effect for RNA replication by constructing a kinetic model that quantitatively explained the behavior of the self-encoding system. Both the experimental and theoretical results consistently indicated that the balance between translation and replication is critical for an efficient self-encoded system, and we determined the optimum balance.

Ultradense synthetic gene brushes on a chip

Dense brushes of linear DNA polymers are assembled on a biochip with approximately 30 nm between anchorage points, amounting to a few mega-base-pairs/microm(3). In bulk solution, a barrier incurs to conjugate more than two end-functionalized DNAs. However, such doublets bind the surface with almost equal efficiency to singlets, suggesting that extended brush buildup reduces the barrier. On-chip transcription reveals that doublets are roughly 2-fold inefficient compared to singlets, a manifestation of the interaction of the enzymatic machinery with the dense brush. Synthetic gene brushes made of DNA conjugates provide simple means to regulate expression on a chip.

A Review of Scanning Probe Microscopy Investigations of Liposome-DNA Complexes

Liposome-DNA complexes are one of the most promising systems for the protection and delivery of nucleic acids to combat neoplastic, viral, and genetic diseases. In addition, they are being used as models in the elucidation of many biological phenomena such as viral infection and transduction. In order to understand these phenomena and to realize the mechanism of nucleic acid transfer by liposome-DNA complexes, studies at the molecular level are required. To this end, scanning probe microscopy (SPM) is increasingly being used in the characterization of lipid layers, lipid aggregates, liposomes, and their complexes with nucleic acid molecules. The most attractive attributes of SPM are the potential to image samples with subnanometer spatial resolution under physiological conditions and provide information on their physical and mechanical properties. This review describes the application of scanning tunneling microscopy and atomic force microscopy, the two most commonly applied SPM techniques, in the characterisation of liposome-DNA complexes.

Evolution and self-assembly of protocells

Cells define the minimal building blocks of life. How cellular life emerged and evolved implies to cross the boundary between living and nonliving matter. Here we explore this problem by presenting several relevant components of the whole picture involving chemistry, physics and natural selection. Available evidence suggests that the basic logic of life can be understood and eventually translated into synthetic forms of cellular life. A simple, physically sound model of information-free protocell replication suggests that the basic logic of how to couple metabolism and container can be more relevant than the specific set of parameters used, thus indicating that the emergence of cells might have been easier than we would expect.

Compositional inheritance: comparison of self-assembly and catalysis

Genetic inheritance in modern cells is due to template-directed replication of nucleic acids. However, the difficulty of prebiotic synthesis of long information-carrying polymers like RNA raises the question of whether some other form of heredity is possible without polymers. As an alternative, the lipid world theory has been proposed, which considers non-covalent assemblies of lipids, such as micelles and vesicles. Assemblies store information in the form of a non-random molecular composition, and this information is passed on when the assemblies divide, i.e. the assemblies show compositional inheritance. Here, we vary several important assumptions of previous lipid world models and show that compositional inheritance is relevant more generally than the context in which it was originally proposed. Our models assume that interaction occurs between nearest neighbour molecules only, and account for spatial segregation of molecules of different types within the assembly. We also draw a distinction between a self-assembly model, in which the composition is determined by mutually favourable interaction energies between the molecules, and a catalytic model, in which the composition is determined by mutually favourable catalysis. We show that compositional inheritance occurs in both models, although the self-assembly case seems more relevant if the molecules are simple lipids. In the case where the assemblies are composed of just two types of molecules, there is a strong analogy with the classic two-allele Moran model from population genetics. This highlights the parallel between compositional inheritance and genetic inheritance.

Life as a nanoscale phenomenon

The nanoscale is not just the middle ground between molecular and macroscopic but a dimension that is specifically geared to the gathering, processing, and transmission of chemical-based information. Herein we consider the living cell as an integrated self-regulating complex chemical system run principally by nanoscale miniaturization, and propose that this specific level of dimensional constraint is critical for the emergence and sustainability of cellular life in its minimal form. We address key aspects of the structure and function of the cell interface and internal metabolic processing that are coextensive with the up-scaling of molecular components to globular nanoobjects (integral membrane proteins, enzymes, and receptors, etc) and higher-order architectures such as microtubules, ribosomes, and molecular motors. Future developments in nanoscience could provide the basis for artificial life.

Double emulsion templated monodisperse phospholipid vesicles

We present a novel approach for fabricating monodisperse phospholipid vesicles with high encapsulation efficiency using controlled double emulsions as templates. Glass-capillary microfluidics is used to generate monodisperse double emulsion templates. We show that the high uniformity in size and shape of the templates are maintained in the final phospholipid vesicles after a solvent removal step. Our simple and versatile technique is applicable to a wide range of phospholipids.

Simulations of electrophoretic RNA transport through transmembrane carbon nanotubes

The study of interactions between carbon nanotubes and cellular components, such as membranes and biomolecules, is fundamental for the rational design of nanodevices interfacing with biological systems. In this work, we use molecular dynamics simulations to study the electrophoretic transport of RNA through carbon nanotubes embedded in membranes. Decorated and naked carbon nanotubes are inserted into a dodecane membrane and a dimyristoylphosphatidylcholine lipid bilayer, and the system is subjected to electrostatic potential differences. The transport properties of this artificial pore are determined by the structural modifications of the membrane in the vicinity of the nanotube openings and they are quantified by the nonuniform electrostatic potential maps at the entrance and inside the nanotube. The pore is used to transport electrophoretically a short RNA segment and we find that the speed of translocation exhibits an exponential dependence on the applied potential differences. The RNA is transported while undergoing a repeated stacking and unstacking process, affected by steric interactions with the membrane headgroups and by hydrophobic interaction with the walls of the nanotube. The RNA is structurally reorganized inside the nanotube, with its backbone solvated by water molecules near the axis of the tube and its bases aligned with the nanotube walls. Upon exiting the pore, the RNA interacts with the membrane headgroups and remains attached to the dodecane membrane while it is expelled into the solvent in the case of the lipid bilayer. The results of the simulations detail processes of molecular transport into cellular compartments through manufactured nanopores and they are discussed in the context of applications in biotechnology and nanomedicine.

From DNA nanotechnology to synthetic biology

Attempts to construct artificial systems from biological molecules such as DNA and RNA by self-assembly are compatible with the recent development of synthetic biology. Genetic mechanisms can be used to produce or control artificial structures made from DNA and RNA, and these structures can in turn be used as artificial gene regulatory elements, in vitro as well as in vivo. Artificial biochemical circuits can be incorporated into cell-like reaction compartments, which opens up the possibility to operate them permanently out of equilibrium. In small systems, stochastic effects become noticeable and will have to be accounted for in the design of future systems.

On the way towards ‘basic autonomous agents’: Stochastic simulations of minimal lipid–peptide cells

In this paper, we apply a recently developed stochastic simulation platform to investigate the dynamic behaviour of minimal 'self-(re-)producing' cellular systems. In particular, we study a set of preliminary conditions for appearance of the simplest forms of autonomy in the context of lipid vesicles (more specifically, lipid-peptide vesicles) that enclose an autocatalytic/proto-metabolic reaction network. The problem is approached from a 'bottom-up' perspective, in the sense that we try to show how relatively simple cell components/processes could engage in a far-from-equilibrium dynamics, staying in those conditions thanks to a rudimentary but effective control of the matter-energy flow through it. In this general scenario, basic autonomy and, together with it, minimal agent systems would appear when (hypothetically pre-biological) cellular systems establish molecular trans-membrane mechanisms that allow them to couple internal chemical reactions with transport processes, in a way that they channel/transform external material-energetic resources into their own means and actively regulate boundary conditions (e.g., osmotic gradients, inflow/outflow of different compounds, ...) that are critical for their constitution and persistence as proto-metabolic cells. The results of our simulations indicate that, before that stage is reached, there are a number of relevant issues that have to be carefully analysed and clarified: especially the immediate effects that the insertion of peptide chains (channel precursors) in the lipid bilayer may have in the structural properties of the membrane (elasticity, permeability, ...) and in the overall dynamic behaviour of the cell.

The autonomy of biological individuals and artificial models

This paper aims to offer an overview of the meaning of autonomy for biological individuals and artificial models rooted in a specific perspective that pays attention to the historical and structural aspects of its origins and evolution. Taking autopoiesis and the recursivity characteristic of its circular logic as a starting point, we depart from some of its consequences to claim that the theory of autonomy should also take into account historical and structural features. Autonomy should not be considered only in internal or constitutive terms, the largely neglected interactive aspects stemming from it should be equally addressed. Artificial models contribute to get a better understanding of the role of autonomy for life and the varieties of its organization and phenomenological diversity.