The Foundry: the DNA synthesis and construction Foundry at Imperial College.

The establishment of a DNA synthesis and construction foundry at Imperial College in London heralds a new chapter in the development of synthetic biology to meet new global challenges. The Foundry employs the latest technology to make the process of engineering biology easier, faster and scalable. The integration of advanced software, automation and analytics allows the rapid design, build and testing of engineered organisms

Statistical Properties of the Interbeat Interval Cascade in Human Subjects

Statistical properties of interbeat intervals cascade are evaluated by considering the joint probability distribution $P(\Delta x_2,\tau_2;\Delta x_1,\tau_1)$ for two interbeat increments $\Delta x_1$ and $\Delta x_2$ of different time scales $\tau_1$ and $\tau_2$. We present evidence that the conditional probability distribution $P(\Delta x_2,\tau_2|\Delta x_1,\tau_1)$ may obey a Chapman-Kolmogorov equation. The corresponding Kramers-Moyal (KM) coefficients are evaluated. It is shown that while the first and second KM coefficients, i.e., the drift and diffusion coefficients, take on well-defined and significant values, the higher-order coefficients in the KM expansion are very small. As a result, the joint probability distributions of the increments in the interbeat intervals obey a Fokker-Planck equation. The method provides a novel technique for distinguishing the two classes of subjects in terms of the drift and diffusion coefficients, which behave differently for two classes of the subjects, namely, healthy subjects and those with congestive heart failure.Comment: 5 pages, 6 figure

Registry of BioBricks Models using CellML

A poster presented at BioSysBio 2007 and at SB3.0One of the main goals in Synthetic Biology is to assess the feasibility of building novel biological systems from interchangeable and standardized parts. In order to collect and share parts, a Registry of standardized DNA BioBricks[1] has been established at MIT. BioBricks can be assembled to form devices and systems to operate in living cells. Design of reliable devices and systems would benefit from accurate models of system function. To predict the function of systems built from many parts, we need to have accurate models for the parts and mechanisms to easily compose those part models into a system model. Therefore, in parallel to increasing the number of parts available and characterising them experimentally, a logical extension to the Registry would be to build a Registry of BioBrick models to complement the physical parts

Solution-processed bilayer photovoltaic devices with nematic liquid crystals

The cross-linking of polymerisable liquid crystalline semiconductors is a promising approach to solution-processable, multilayer, organic photovoltaics. Here we demonstrate an organic bilayer photovoltaic with an insoluble electron-donating layer formed by cross-linking a nematic reactive mesogen. We investigate a range of perylene diimide (PDI) materials, some of which are liquid crystalline, as the overlying electron acceptor layer. We find that carrier mobility of the acceptor materials is enhanced by liquid crystallinity and that mobility limits the performance of photovoltaic devices. © 2013 © 2013 Taylor & Francis

Layering genetic circuits to build a single cell, bacterial half adder

Background: Gene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. Here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits. Results: Using a synthetic biology approach that is supported by computational modelling and rigorous characterisation, AND, OR and NOT biological logic gates were layered in both parallel and serial arrangements to generate a repertoire of Boolean operations that include NIMPLY, XOR, half adder and half subtractor logics in a single cell. Subsequent evaluation of these near-digital biological systems revealed critical design pitfalls that triggered genetic context-dependent effects, including 5′ UTR interferences and uncontrolled switch-on behaviour of the supercoiled σ54 promoter. In particular, the presence of seven consecutive hairpins immediately downstream of the promoter transcription start site severely impeded gene expression. Conclusions: As synthetic biology moves forward with greater focus on scaling the complexity of engineered genetic circuits, studies which thoroughly evaluate failure modes and engineering solutions will serve as important references for future design and development of synthetic biological systems. This work describes a representative case study for the debugging of genetic context-dependent effects through principles elucidated herein, thereby providing a rational design framework to integrate multiple genetic circuits in a single prokaryotic cell.Published versio

Comprehensive web-based broker for bio-technology design and manufacturing

Synthetic biology, particularly in relation to characterisation experiments relating to the description of bio-parts frequently involves the use of a wide range of equipment, including, for example, plate reader's, flow cytometers, and mass spectrometers. This equipment is often from multiple manufacturers. The study describes broker technology that has been developed which has the ability to connect multiple types of equipment into a common information environment; the connectivity from the databases and equipment is achieved using Visbion's ‘cube’ technology that involves military specification encryption for data security. The broker technology uses a new, developing standard, Digital Imaging and Communication in Medicine (DICOM)-SB, that is based on the highly successful international standard for biomedicine, DICOM. The broker uses a version of the DICOM data model that has been specifically designed for synthetic biology and, in particular, characterisation data

Implications of flexible spacer rotational processes on the liquid crystal behavior of 4,5-dihydroisoxazole benzoate dimers

The synthesis of some novel non-symmetric liquid crystal dimers, {3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-(decyloxy)benzoates (5a–d) and 4-{3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-{[6-(octyloxy)naphthalen-2-yl]ethynyl}benzoate (9a–d), are reported. The liquid-crystalline properties, theoretical calculations based on the conformational aspects of the flexible alkyl spacer and X-ray experiments are discussed. The syntheses of the key intermediates, 2-{3-[4-(octyloxy)phenyl]-4,5-dihydroisoxazol-5-yl}alkanol (3a–d), presenting the flexible alkyl spacer were achieved through [3+2] cycloaddition reactions between nitrile oxides, which were generated in situ by oxidation of the respective aromatic oximes, and dipolarophile alkenols (CH2[double bond, length as m-dash]CH(CH2)nOH, n = 1, 2, 3, and 4). The benzoates 5a–d were synthesized through esterification of 3a–d and p-n-decyloxybenzoic acid (4). The esters 9a–d were synthesized through derivatization of isoxazolines 3a–d into 4-{3-[4-(octyloxyphenyl)]-4,5-dihydroisoxazol-5-yl}alkyl 4-bromobenzoate (7a–d) followed by a Sonogashira reaction with 2-ethynyl-6-octyloxynaphthalene (8). 5a and 5b showed a monotropic smectic C phase. 9a/c displayed a enantiotropic nematic (N) mesophase, whereas 9b/d showed a monotropic nematic mesophase. No mesophase was observed for 7a–d. An odd–even effect was observed for 5a–d and 9a–d associated with the crystal to isotropic phase transition and crystal to nematic phase, respectively, as the length of the spacer was increased from 1 to 4 carbon atoms. The transitional properties were higher for odd-numbered members (n = 1 and 3) for all of the series studied. The X-ray data of compounds 5a and 5b are in agreement with polarizing optical microscopy observations with the assignment of an SmC mesophase. Density functional theory calculations using the B3LYP hybrid functional with the level 6-311G(d,p) basis set were performed for molecules 5a–d to correlate the conformation of the flexible spacer and the transitional properties. The conformational analysis showed that the most stable conformation for 5a–d is one where all of the carbon atoms of the flexible spacer are orientated at 180° (antiperiplanar orientation) except for 5a because the spacer is too short. The odd-numbered members have a more bent shape and are less elongated molecules than the even-numbered members. Thus, mesomorphic behavior is dictated by the conformational constraint imposed by the flexible spacer on the mesogenic groups

Developing synthetic biology for industrial biotechnology applications

Since the beginning of the 21st Century, synthetic biology has established itself as an effective technological approach to design and engineer biological systems. Whilst research and investment continues to develop the understanding, control and engineering infrastructural platforms necessary to tackle ever more challenging systems — and to increase the precision, robustness, speed and affordability of existing solutions — hundreds of start-up companies, predominantly in the US and UK, are already translating learnings and potential applications into commercially viable tools, services and products. Start-ups and SMEs have been the predominant channel for synthetic biology commercialisation to date, facilitating rapid response to changing societal interests and market pull arising from increasing awareness of health and global sustainability issues. Private investment in start-ups across the US and UK is increasing rapidly and now totals over $12bn. Health-related biotechnology applications have dominated the commercialisation of products to date, but significant opportunities for the production of bio-derived materials and chemicals, including consumer products, are now being developed. Synthetic biology start-ups developing tools and services account for between 10% (in the UK) and ∼25% (in the US) of private investment activity. Around 20% of synthetic biology start-ups address industrial biotechnology targets, but currently, only attract ∼11% private investment. Adopting a more networked approach — linking specialists, infrastructure and ongoing research to de-risk the economic challenges of scale-up and supported by an effective long-term funding strategy — is set to transform the impact of synthetic biology and industrial biotechnology in the bioeconomy

A Forward-Design Approach to Increase the Production of Poly-3-Hydroxybutyrate in Genetically Engineered Escherichia coli

Biopolymers, such as poly-3-hydroxybutyrate (P(3HB)) are produced as a carbon store in an array of organisms and exhibit characteristics which are similar to oil-derived plastics, yet have the added advantages of biodegradability and biocompatibility. Despite these advantages, P(3HB) production is currently more expensive than the production of oil-derived plastics, and therefore, more efficient P(3HB) production processes would be desirable. In this study, we describe the model-guided design and experimental validation of several engineered P(3HB) producing operons. In particular, we describe the characterization of a hybrid phaCAB operon that consists of a dual promoter (native and J23104) and RBS (native and B0034) design. P(3HB) production at 24 h was around six-fold higher in hybrid phaCAB engineered Escherichia coli in comparison to E. coli engineered with the native phaCAB operon from Ralstonia eutropha H16. Additionally, we describe the utilization of non-recyclable waste as a low-cost carbon source for the production of P(3HB)

Debugging experiment machinery through time-course event sequence analysis

This application note describes an open-source web application software package for viewing and analysing time-course event sequences in the form of log files containing timestamps. Web pages allow the visualisation of time-course event sequences as time curves and the comparison of sequences against each other to visualise deviations between the timings of the sequences. A feature allows the analysis of the sequences by parsing selected sections with a support vector machine model that heuristically calculates a value for the likelihood of an error occurring based on the textual output in the log files. This allows quick analysis for errors in files with large numbers of log events. The software is written in ASP.NET with Visual Basic code-behind to allow it to be hosted on servers and integrated into web application frameworks