Replicability and Recurrence in the Experimental Evolution of a Group I Ribozyme

In order to explore the variety of possible responses available to a ribozyme population evolving a novel phenotype, five Tetrahymena thermophila group I intron ribozyme pools were evolved in parallel for cleavage of a DNA oligonucleotide. These ribozyme populations were propagated under identical conditions and characterized when they reached apparent phenotypic plateaus; the populations that reached the highest plateau showed a near 100-fold improvement in DNA cleavage activity. A detailed characterization of the evolved response in these populations reveals at least two distinct phenotypic trajectories emerging as a result of the imposed selection. Not only do these distinct solutions exhibit differential DNA cleavage activity, but they also exhibit a very different correlation with a related, but unselected, phenotype: RNA cleavage activity. In turn, each of these trajectories is underwritten by differing genotypic profiles. This study underscores the complex network of possible trajectories through sequence space available to an evolving population and uncovers the diversity of solutions that result when the process of experimental evolution is repeated multiple times in a simple, engineered system

A hybrid camphor-camphene wax material for studies on self-propelled motion.

A new material that combines self-propelled motion with wax-like mechanical properties and can be formed into non-trivial shapes is presented

Creating and Maintaining Chemical Artificial Life by Robotic Symbiosis

We present a robotic platform based on the open source RepRap 3D printer that can print and maintain chemical artificial life in the form of a dynamic, chemical droplet. The robot uses computer vision, a self-organizing map, and a learning program to automatically categorize the behavior of the droplet that it creates. The robot can then use this categorization to autonomously detect the current state of the droplet and respond. The robot is programmed to visually track the droplet and either inject more chemical fuel to sustain a motile state or introduce a new chemical component that results in a state change (e.g., division). Coupling inexpensive open source hardware with sensing and feedback allows for replicable real-time manipulation and monitoring of nonequilibrium systems that would be otherwise tedious, expensive, and error-prone. This system is a first step towards the practical confluence of chemical, artificial intelligence, and robotic approaches to artificial life

Spontaneous formation of liquid crystalline phases and phase transitions in highly concentrated plasmid DNA

The liquid crystalline (LC) properties of two supercoiled plasmid DNA samples, pBSK (2958 bp) and pGEM (3000 bp), have been studied using polarised light microscopy (PLM), circular dichroism (CD) and UV-Vis spectroscopy. The influence of methods of isolation on plasmid LC behaviour is described, and using PLM we have demonstrated the spontaneous formation of cholesteric fingerprint-like textures. Preliminary studies of LC phase transitions in pGEM show the irreversibility of LC phase formation, as a consequence of changes in the tertiary structure of supercoiled plasmids. Using UV-Vis spectroscopy a hyperchromic effect was observed with increasing temperature. The CD spectra clearly showed structural changes, and probably mismatching of DNA bases, during cooling. Finally, we have observed an irreversible phase transition in plasmid DNA which is very different from that previously reported in linear DNA

Transport of Live Cells under Sterile Conditions Using a Chemotactic Droplet

© 2018 The Author(s). 1-Decanol droplets, formed in an aqueous medium containing decanoate at high pH, become chemotactic when a chemical gradient is placed in the external aqueous environment. We investigated if such droplets can be used as transporters for living cells. We developed a partially hydrophobic alginate capsule as a protective unit that can be precisely placed in a droplet and transported along chemical gradients. Once the droplets with cargo reached a defined final destination, the association of the alginate capsule and decanol droplet was disrupted and cargo deposited. Both Escherichia coli and Bacillus subtilis cells survived and proliferated after transport even though transport occurred under harsh and sterile conditions

Regenerated silk fibroin membranes as separators for transparent microbial fuel cells

Abstract In recent years novel applications of bioelectrochemical systems are exemplified by phototrophic biocathodes, biocompatible enzymatic fuel cells and biodegradable microbial fuel cells (MFCs). Herein, transparent silk fibroin membranes (SFM) with various fibroin content (2%, 4% and 8%) were synthesised and employed as separators in MFCs and compared with standard cation exchange membranes (CEM) as a control. The highest real-time power performance of thin-film SFM was reached by 2%-SFM separators: 25.7 ± 7.4 μW, which corresponds to 68% of the performance of the CEM separators (37.7 ± 3.1 μW). Similarly, 2%-SFM revealed the highest coulombic efficiency of 6.65 ± 1.90%, 74% of the CEM efficiency. Current for 2%-SFM reached 0.25 ± 0.03 mA (86% of CEM control). Decrease of power output was observed after 23 days for 8% and 4% and was a consequence of deterioration of SFMs, determined by physical, chemical and biological studies. This is the first time that economical and transparent silk fibroin polymers were successfully employed in MFCs

Structure of laponite-styrene precursor dispersions for production of advanced polymer-clay nanocomposites

One method for production of polymer-clay nanocomposites involves dispersal of surface-modified clay in a polymerisable monomeric solvent, followed by fast in situ polymerisation. In order to tailor the properties of the final material we aim to control the dispersion state of the clay in the precursor solvent. Here, we study dispersions of surface-modified Laponite, a synthetic clay, in styrene via large-scale Monte-Carlo simulations and experimentally, using small angle X-ray and static light scattering. By tuning the effective interaction between simulated laponite particles we are able to reproduce the experimental scattering intensity patterns for this system, with good accuracy over a wide range of length scales. However, this agreement could only be obtained by introducing a permanent electrostatic dipole moment into the plane of each Laponite particle, which we explain in terms of the distribution of substituted metal atoms within each Laponite particle. This suggests that Laponite dispersions, and perhaps other clay suspensions, should display some of the structural characteristics of dipolar fluids. Our simulated structures show aggregation regimes ranging from networks of long chains to dense clusters of Laponite particles, and we also obtain some intriguing ‘globular’ clusters, similar to capsids. We see no indication of any ‘house-of-cards’ structures. The simulation that most closely matches experimental results indicates that gel-like networks are obtained in Laponite dispersions, which however appear optically clear and non-sedimenting over extended periods of time. This suggests it could be difficult to obtain truly isotropic equilibrium dispersion as a starting point for synthesis of advanced polymer-clay nanocomposites with controlled structures

A comprehensive study of custom-made ceramic separators for microbial fuel cells: Towards "living" bricks

Towards the commercialisation of microbial fuel cell (MFC) technology, well-performing, cost-effective, and sustainable separators are being developed. Ceramic is one of the promising materials for this purpose. In this study, ceramic separators made of three different clay types were tested to investigate the effect of ceramic material properties on their performance. The best-performing ceramic separators were white ceramic-based spotty membranes, which produced maximum power outputs of 717.7 ± 29.9 µW (white ceramic-based with brown spots, 71.8 W·m−3) and 715.3 ± 73.0 µW (white ceramic-based with red spots, 71.5 W·m−3). For single material ceramic types, red ceramic separator generated the highest power output of 670.5 ± 64. 8 µW (67.1 W·m−3). Porosity investigation revealed that white and red ceramics are more porous and have smaller pores compared to brown ceramic. Brown ceramic separators under performed initially but seem more favourable for long-term operation due to bigger pores and thus less tendency of membrane fouling. This study presents ways to enhance the function of ceramic separators in MFCs such as the novel spotty design as well as fine-tuning of porosity and pore size

Nonlinear absorption and nonlinear refraction: Maximizing the merit factors

Both nonlinear absorption and nonlinear refraction are effects that are potentially useful for a plethora of applications in photonics, nanophotonics and biophotonics. Despite substantial attention given to these phenomena by researchers studying the merits of disparate systems such as organic materials, hybrid materials, metal-containing molecules and nanostructures, it is virtually impossible to compare the results obtained on different materials when varying parameters of the light beams and different techniques are employed. We have attempted to address the problem by studying the properties of various systems in a systematic way, within a wide range of wavelengths, and including the regions of onephoton, two-photon and three-photon absorption. The objects of our studies have been typical nonlinear chromophores, such as π-conjugated molecules, oligomers and polymers, organometallics and coordination complexes containing transition metals, organometallic dendrimers, small metal-containing clusters, and nanoparticles of various kinds, including semiconductor quantum dots, plasmonic particles and rare-earth doped nanocrystals. We discuss herein procedures to quantify the nonlinear response of all of these systems, by defining and comparing the merit factors relevant for various applications