Team:UCL/Humans/Collab

How it all began: Making sense of antisense together!

The RewirED Edinburgh Team focused on the creation of a metabolic wiring system as a novel way of connecting logic gates in different bacterial strains. They developed a software tool to analyze sequences of antisense RNA for gene silencing which identifies the optimal sequence (~100bp, covering RBS and start codon) and analyses the structure to find the most stable antisense RNA.
In this collaboration they provided the sequence of the antisense gene which, according to their model, has the fewest secondary structures in the core regions and analysed the behaviour of our design of an antisense gene.

From our side we provided real world data on the behaviour of the antisense gene silencing in order to test the accuracy of their model and efficacy of their software. Specifically we analysed the growth in different media of E. coli engineered with the antisense gene silencing BioBrick . The silenced gene is core for the survival of E. coli and the reduction in growth corresponds to the efficacy of the antisense. We sent them all the data we gathered that they could then compare to their in silico prediction.
The sequence we designed didn't effectively repress growth in E.coli as modelled by the software. We designed new primers to amplify the sequence suggested by Edinburgh: a smaller fragment with better predicted functionality, and we are now in the stage of cloning and testing it to provide them with more data on their software's effectiveness.


Identification of the optimal antisense RNA for ispB silencing

Analysis of our antisense RNA design for ispB silencing

The Microbial & Enzyme Technology Lab led by Dr Lígia O. Martins at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, is one of the world leaders in bioremediation with microorganisms and enzymes. Their paper titled 'Synergistic action of azoreductase and laccase leads to maximal decolourization and detoxification of model dye-containing wastewaters' [1] was the fundamental inspiration for our Goodbye AzoDye project. We are truly grateful for their initial support and guidance, and for sending us the following plasmids for our experiments:

pAzoR (pLP-1) containing the FMN-dependent NADH-azoreductase 1 gene. [2]
pCotA (pLOM10) containing the Spore Coat Protein Laccase gene. [3]
p1B6 containing the mutant FMN-dependent NADH-azoreductase 1 gene [4]
pBsDyp (pRC-2) containing the Dye Decolourising Peroxidase BSU38260 gene. [5]
pPpDyp (pRC-1) containing the Dye Decolourising Peroxidase PP_3248 gene.[5]

We approached the Central St Martins textiles department with our ideas of synthetic biology and science and they asked ‘When does technology like this become accessible?’ This question yielded a set of beautiful visualisation of the way our bacteria could be used to create art if controlled by light. These pieces by second year Textiles Design BA students Cameo Bondy and Barbara Czepiel exhibit the textiles that could be created if our bacteria contained optogenetic biobricks that switched their dye breakdown capacities on and off via light cues.

A practicing independent designer and researcher, Natsai Audrey Chieza is a Design Futurist inspired by material innovation and technology. Natsai considers her creative pursuits with a strong interest in how the life sciences can enable new craft processes for a more robust environmental paradigm.

Natsai contributed a series of pieces to be displayed at the #UncolourMeCurious from her Faber Futures exhibition, exploring the use of bacteria to create pigments and dye fabrics, deviating from the standardisation of a petri dish.

Natsai has achieved measurable success in design research projects for Microsoft, Nissan, Unilever and EDF Energy. She has also exhibited in numerous design exhibitions and events across Europe including the Victoria & Albert Muesum, London; Audax Textile Museum, Tilburg; Salone Internazionale del Mobile di Milano, Milan; Designersblock LDF, London; EN VIE/ ALIVE, Paris; Science Gallery, Dublin; and Heimtextil, Frankfurt.