Programme

Summaries

Richard Mayne & Andy Adamatzky: Collision-based computing implemented with calcium-containing vesicles in a myxomycete model

Collision-based computing (CBC) is a form of unconventional computing in which travelling objects represent data and conditional routing of signals via object collisions determines the output state. We present experimental observations of the rapid transport and subsequent collisions between calcium-containing vesicles within the plasmodium of slime mould Physarum polycephalum and characterise these phenomena as the first intracellular realisation of CBC. We proceed to discuss the implications of these findings and practical considerations for "useful" vesicle collision circuit design. Our findings are relevant to all fields of scientific inquiry where biology and computer science meet.

Martyn Amos: Population-based microbial computing: a third wave of synthetic biology?

Synthetic biology is an emerging research field, in which engineering principles are applied to natural, living systems. A major goal of synthetic biology is to harness the inherent “biological nanotechnology” of living cells for the purposes of computation, production or diagnosis. As the field evolves, it is gradually developing from a single-cell approach (akin to using standalone computers) to a distributed, population-based approach (akin to using networks of connected machines). We anticipate this eventually representing the “third wave” of synthetic biology (the first two waves being the emergence of modules and systems, respectively, with the second wave still yet to peak). In this talk we review the developments that are leading to this third wave, and describe some of the existing scientific and technological challenges.

Jonathan Naylor, Harold Fellermann & Natalio Krasnogor: Physical modelling exploring the self-organising behaviour of synthetic and natural biofilms

To facilitate the understanding of biofilm self-organisation and inform the development of novel synthetic biofilms, computational models can be developed. Many different models exist for capturing a variety of biofilms, yet a standard modelling approach or tool has not yet been conceived. The creation of such a generic tool is what we propose in this research, developing a multiscale modelling platform through which we will demonstrate the capacity for simulation to accurately capture and predict biofilm behaviour.

Savas Konur, Mariam Kiran, Marian Gheorghe & Omer Markovitch: Analysing Synthetic Bacteria Colonies: An Agent-based Approach

We discuss the agent-based modelling and simulation approach to analyse large bacterial colonies formed by many individual synthetic cells. We discuss the advantages and current limitations of the approach when modelling biological models.

Friedrich C. Simmel: Programming molecular structures and processes using DNA

Maybe the most important feature of biopolymers such as DNA, RNA and proteins is that they can be regarded as information-encoding strings of molecular "letters". As these letters can be connected into strings in an arbitrary order, a vast combinatorial number of different "messages" can be generated. Depending on the context, these messages may mean something - for instance, DNA may code for a protein, a functional RNA molecule, or for a DNA nanostructure. Molecular programmers would now like to learn how to efficiently generate sequences that produce a desired (synthetic) biological structure or process - i.e., program biology using molecular code. In this talk, we will discuss a few of our own efforts along these lines, ranging from DNA nanostructures over in vitro biochemical circuits to in vivo synthetic biology.

Goksel Misirli, Jennifer Hallinan, Owen Gilfellon & Anil Wipat: A standard model repository for genetic design automation

One ambition of synthetic biology is the large-scale engineering of biological systems. However, as the complexity and size of designs increases, the manual design of genetic circuits becomes more challenging. Computational tools often use libraries of mathematical models of biological parts in order to aid the user in building complex and predictable designs. To support automated, model-driven design it is desirable that in silico models are modular, composable and in standard formats. Here, we present an approach for composable and modular models for synthetic biology, termed standard virtual parts (SVPs), to support software tools in model-driven process. A repository of SVPs has been established to facilitate computational genetic circuit design.

Aurore Dupin & Friedrich C. Simmel: Biochemical circuits in cell-sized microcompartments

In an effort to model the compartmentalization of chemical processes within biological cells, we aim at the encapsulation of synthetic in vitro transcription circuits into networks of communicating droplets. The compartments consist of aqueous droplets surrounded by a monolayer of lipids, which form a bilayer interface when brought into contact. Biological pores can incorporate into this bilayer and allow for the specific translocation of chemicals based on their size and charge. The genelet circuits are activated by the diffusion of chosen chemicals through this network. Unlike in bulk systems, chemical pathways can thus be separated or coupled controllably both in space and time.

Jerzy Kozyra, Chien-Yi Chang, Alessandro Ceccarelli, Harold Fellermann & Natalio Krasnogor: Programming synthetic scaffolds for DNA origami

Scaffolded DNA origami is one of the most successful methods allowing precise matter arrangement and manipulation on a nano-scale. The nanostructures are realised through rational programming of short oligos which fold a long viral DNA called the ’scaffold’ strand. Here we propose a generalisation of the origami programmability which will now also include manufacturing protocol for purely synthetic scaffolds. We developed a strategy for de novo generation of long artificial DNA sequences which are uniquely addressable and biologically inert. Next, we show how they can be used as either DNA scaffolds or transcribed RNA scaffolds for origami systems. This new method not only allows building nanostructures which are programmed for a specific functionality but is also far more feasible for novel applications in Synthetic Biology.

Matthaeus Schwarz-Schilling, Fabio Chizzolini, Andrea Muckl, Sheref Mansy, Friedrich C. Simmel: Cell-free production and assembly of a multifunctional RNA-protein hybrid structure

In order to study the dynamics of the self-assembly of a RNA-protein hybrid structure in a cell-free transcription-translation system, we encoded an RNA nanostructure with peptide binding aptamers and three proteins into a plasmid. The RNA structure is comprised of a three-way junction with three differently functionalized arms so that each report a different step in the structure’s self-organization process. The first arm reports the concentration of correctly folded RNA-scaffold. The second arm directs the assembly of a fluorescent protein-based FRET pair. The third subunit localizes the assembled nanostructure at streptavidin-coated surfaces. Our work demonstrates the use of a cell-free gene expression system for prototyping and optimizing the assembly of biomolecular hybrid structures that can later be transferred into bacteria.