427 research outputs found
Systems chemistry: all in a spin
The authors thank the Leverhulme Trust for an award (RPG-2013-343) to support LC.A fundamental challenge in supramolecular systems chemistry is to engineer the emergence of complex behaviour. The collective structures of metal cyanide chains have now been interpreted in the same manner as the myriad of magnetic phases displayed by frustrated spin systems, highlighting a symbiotic approach between systems chemistry and magnetism.PostprintPeer reviewe
Selection for Replicases in Protocells
PMCID: PMC3649988This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Electrostatically gated membrane permeability in inorganic protocells
Although several strategies are now available to produce functional microcompartments analogous to primitive cell-like structures, little progress has been made in generating protocell constructs with self-controlled membrane permeability. Here we describe the preparation of water-dispersible colloidosomes based on silica nanoparticles and delineated by a continuous semipermeable inorganic membrane capable of self-activated, electrostatically gated permeability. We use crosslinking and covalent grafting of a pH-responsive copolymer to generate an ultrathin elastic membrane that exhibits selective release and uptake of small molecules. This behaviour, which depends on the charge of the copolymer coronal layer, serves to trigger enzymatic dephosphorylation reactions specifically within the protocell aqueous interior. This system represents a step towards the design and construction of alternative types of artificial chemical cells and protocell models based on spontaneous processes of inorganic self-organization
On RAF Sets and Autocatalytic Cycles in Random Reaction Networks
The emergence of autocatalytic sets of molecules seems to have played an
important role in the origin of life context. Although the possibility to
reproduce this emergence in laboratory has received considerable attention,
this is still far from being achieved. In order to unravel some key properties
enabling the emergence of structures potentially able to sustain their own
existence and growth, in this work we investigate the probability to observe
them in ensembles of random catalytic reaction networks characterized by
different structural properties. From the point of view of network topology, an
autocatalytic set have been defined either in term of strongly connected
components (SCCs) or as reflexively autocatalytic and food-generated sets
(RAFs). We observe that the average level of catalysis differently affects the
probability to observe a SCC or a RAF, highlighting the existence of a region
where the former can be observed, whereas the latter cannot. This parameter
also affects the composition of the RAF, which can be further characterized
into linear structures, autocatalysis or SCCs. Interestingly, we show that the
different network topology (uniform as opposed to power-law catalysis systems)
does not have a significantly divergent impact on SCCs and RAFs appearance,
whereas the proportion between cleavages and condensations seems instead to
play a role. A major factor that limits the probability of RAF appearance and
that may explain some of the difficulties encountered in laboratory seems to be
the presence of molecules which can accumulate without being substrate or
catalyst of any reaction.Comment: pp 113-12
Preparation of Large Monodisperse Vesicles
Preparation of monodisperse vesicles is important both for research purposes and for practical applications. While the extrusion of vesicles through small pores (∼100 nm in diameter) results in relatively uniform populations of vesicles, extrusion to larger sizes results in very heterogeneous populations of vesicles. Here we report a simple method for preparing large monodisperse multilamellar vesicles through a combination of extrusion and large-pore dialysis. For example, extrusion of polydisperse vesicles through 5-µm-diameter pores eliminates vesicles larger than 5 µm in diameter. Dialysis of extruded vesicles against 3-µm-pore-size polycarbonate membranes eliminates vesicles smaller than 3 µm in diameter, leaving behind a population of monodisperse vesicles with a mean diameter of ∼4 µm. The simplicity of this method makes it an effective tool for laboratory vesicle preparation with potential applications in preparing large monodisperse liposomes for drug delivery
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
Integrated information increases with fitness in the evolution of animats
One of the hallmarks of biological organisms is their ability to integrate
disparate information sources to optimize their behavior in complex
environments. How this capability can be quantified and related to the
functional complexity of an organism remains a challenging problem, in
particular since organismal functional complexity is not well-defined. We
present here several candidate measures that quantify information and
integration, and study their dependence on fitness as an artificial agent
("animat") evolves over thousands of generations to solve a navigation task in
a simple, simulated environment. We compare the ability of these measures to
predict high fitness with more conventional information-theoretic processing
measures. As the animat adapts by increasing its "fit" to the world,
information integration and processing increase commensurately along the
evolutionary line of descent. We suggest that the correlation of fitness with
information integration and with processing measures implies that high fitness
requires both information processing as well as integration, but that
information integration may be a better measure when the task requires memory.
A correlation of measures of information integration (but also information
processing) and fitness strongly suggests that these measures reflect the
functional complexity of the animat, and that such measures can be used to
quantify functional complexity even in the absence of fitness data.Comment: 27 pages, 8 figures, one supplementary figure. Three supplementary
video files available on request. Version commensurate with published text in
PLoS Comput. Bio
Emergence of light-driven protometabolism on recruitment of a photocatalytic cofactor by a self-replicator
Establishing how life can emerge from inanimate matter is among the grand challenges of contemporary science. Chemical systems that capture life’s essential characteristics—replication, metabolism and compartmentalization—offer a route to understanding this momentous process. The synthesis of life, whether based on canonical biomolecules or fully synthetic molecules, requires the functional integration of these three characteristics. Here we show how a system of fully synthetic self-replicating molecules, on recruiting a cofactor, acquires the ability to transform thiols in its environment into disulfide precursors from which the molecules can replicate. The binding of replicator and cofactor enhances the activity of the latter in oxidizing thiols into disulfides through photoredox catalysis and thereby accelerates replication by increasing the availability of the disulfide precursors. This positive feedback marks the emergence of light-driven protometabolism in a system that bears no resemblance to canonical biochemistry and constitutes a major step towards the highly challenging aim of creating a new and completely synthetic form of life. [Figure not available: see fulltext.]
Social and ethical checkpoints for bottom-up synthetic biology, or protocells
An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints
- …