Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

BACKGROUND: Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. RESULTS: We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. CONCLUSIONS: Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly

A Biobrick Library for Cloning Custom Eukaryotic Plasmids

Researchers often require customised variations of plasmids that are not commercially available. Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. We illustrate the collection by building several model contructs, including concatemers of protein binding-site motifs, and a variety of plasmids for eukaryotic stable cloning and chromosomal insertion. For example, in 3 biobrick iterations, we make a cerulean-reporter plasmid for cloning fluorescent protein fusions. Furthermore, we use the collection to implement a recombinase-mediated DNA insertion (RMDI), allowing chromosomal site-directed exchange of genes. By making one recipient stable cell line, many standardised cell lines can subsequently be generated, by fluorescent fusion-gene exchange. We propose that this biobrick collection may be distributed peer-to-peer as a stand-alone library, in addition to its distribution through the Registry of Standard Biological Parts (http://partsregistry.org/)

Water sprinkling market pigs in a stationary trailer. 1. Effects on pig behaviour, gastrointestinal tract temperature and trailer micro-climate

Pigs are often transported to slaughter under conditions outside their thermo-neutral zones, which can lead to reduced welfare and increased losses. Water sprinkling in barns is used to control microclimate resulting in pig body temperature reduction and improved welfare; however there is no clear evidence of these effects during transport. The aim of this study was to observe the effect of sprinkling pigs in trailers on behaviour and body temperature during transport and lairage, as well as to observe the effects on trailer microclimate e. In each of 12 weeks, 2 pot-belly trailers with 208 pigs each (n=4,992) were transported from the same farm on the same day 2 h to slaughter. One trailer was equipped with sprinklers that ran for 5 min ( 3c125 L) before departure and before unloading, the other trailer served as the control. In each trailer, 4 compartments were outfitted with cameras, ammonia detectors and temperature/humidity data loggers. The gastrointestinal tract temperature (GTT; \ub0C) of 4 randomly chosen pigs (n=384) in each test compartment was recorded using orally administered data loggers. Trailer and deck loading order were randomized. Behaviour during transport, unloading and lairage was recorded from video or live observations. Data were analyzed through ANOVA with ambient temperature external to the trailer (AmbT) as a covariate. AmbT averaged 19.5 \ub0C\ub13.8 \ub0C (range: 13.6 to 25.8 \ub0C). Sprinkled trailers showed lower (P=0.002) increases in internal compartment temperature from loading to unloading, smaller (P23 \ub0C, there was no effect of sprinkling on behaviour on the trailer, but at AmbT24 \ub0C (P=0.08). These data suggest that sprinkling pigs in a stationary vehicle when AmbT exceeds 23 \ub0C has the potential to prevent increases in body temperature during short duration transport without detrimental effects on ammonia levels or behaviour during unloading