tools and methods for enhanced metrology in synthetic biology

There has been a larger emphasis since 2016 on the need for more technical standards to
support the expansion of synthetic biology. The development of the BASIC assembly and
Bio-bricks has taken the first steps to achieving a greater level of standardistaion, however
there is still a lot to be done in order to make synthetic biology truly viable on an industrial
level.
The aim of this project is to use metrology to improve the accuracy and comparability of
synthetic biology. This will be done by looking at areas of the current BASIC assembly
protocol and analysis in order to locate areas which can make a large impact by the
introduction of standards and/or standardised units.
BioBrick Assembly was the first step taken within synthetic biology to overcome the
overwhelming lack of standardisation in synthetic biology. This is due to the use of
standardised BioBricks which conform to a restriction-enzyme assembly standard. This
means that the synthetic biology process is to a high degree standardised at the molecular
and cellular level. On the other hand there has been no real progress in viable
standardisation of larger scale processes and measurement processes.
Currently the measurement of fluorescents in order to quantitatively validate success of
assembly is seriously limited. There is a serious lack of a standardised measurement of
fluorescence, instead measurements are taken relative to the other samples within the
experiment. This severely limits the both inter-experimental and inter-laboratory
comparison and thus limits progress. This limitation is facilitated by lack of equipment and
limits on funding in laboratories.
A potential resolution to this is to produce a fluorescein based standard. Fluorescein is
not expensive Approx. 0.35 GBP per gram and it has been shown to be a useful
fluorophore for testing the precision of nanoliter dispensing.
On the other hand the
fluorescein signal is also highly dependent on the fluorescence reader. This can however
be counteracted by finding the appropriate concentration range before performing the
calibration of the plate reader using a standard curve. This PhD will seek to introduce a
standard Fluorescence Unit to facilitate inter-laboratory comparison. This will be done
using fluorescein to create a standard curve by which absorption can be converted into
fluorescein concentration units.
The ability to upscale processes through automation both precisely and reliably is very
important to the future of synthetic biology. The use of appropriate standard equipment and
protocol is very important when creating any engineering protocol but this is especially
important in biological fields where the sensitivity of biological systems to even small
changes in cellular and/or environmental context can have a large impact on outcome.
This is why the autonomous process must be optimized at each step of the process. This
is done both by programming such as expiration speed and position in which liquid is
dispensed and in more physical ways such as using appropriate size pipette tips and liquid
containers as well as standardizing the initial OD of each sample. This is something that I
will also address in my PhD by looking at each step of our current BASIC assembly
process in turn and seeing if changes in the aforementioned equipment and processes
have a significant impact on the protocols outcome.