Advanced Modules (Second Term)

Advanced Modules 

 Synthetic Circuit Design: This course will cover modelling and analysis of synthetic genetic circuits. Topics covered will include logic circuits, standardization and registry of standard biological parts, libraries and chassis and the engineering design test cycle. Tools including CAD tools, Eugene, Clotho, BioFAB, GEC Compilers, Snapgene will be covered as well as best implementation of designs. In the second week information will be provided on promoter engineering and promoter interference/inducible expression, translation and RNA secondary structure, RBS and codon usage, CRISPR/RNA silencing, RNA circuits/riboswitches and ultimately protein engineering, maturation and degradation. Wetlab practical sessions will be spread throughout the 2 weeks.

(Core module. Duration: two weeks)

Advanced Experimental Techniques (during project weeks at Bristol and Warwick): Students will learn how specialist equipment and capabilities are being used to study biological molecules and cells. Ongoing research includes light, atomic force and electron microscopy including correlative light electron microscopy, nuclear magnetic resonance, X-ray crystallography, Fourier transform infrared spectroscopy, circular dichroism, analytical ultracentrifugation, Isothermal titration calorimetry, microfluidics, etc. They will also hear how high-throughput protein and cell engineering can be done with the help of liquid handling and protein crystallization robots, and flow cytometry. Students will meet staff that run facilities, learn how research results are generated, as well as attending hands-on sessions.

(Advanced module. Duration: two weeks)

Cellular Design I: This module will introduce some of the concepts, technologies and techniques, which can allow the design and engineering of novel cellular functionality. The week will begin with lectures on flux in metabolic networks, describing the process of going from analysis to manipulation and engineering metabolism. This will be followed by Gene Cluster Discovery and Combinatorial Engineering of Metabolism. Lectures on Directed Evolution as a tool will introduce the basic notions and the use of evolution as a design tool in synthetic biology .. Lastly, this module will cover genome minimization and advanced genome editing.

(Core module. Duration: one week)

Biomimetic Construction I: The basic concepts behind the natural production, synthesis, modification of polypeptides and nucleic acids will be explained in addition to nanostructures and assemblies and protein engineering and design. In particular, topics to be explored will include  Protocells, Functional complexes in membranes, Natural protein production and modification, Applications of modified nucleic acids and Making Prokaryotic and Eukaryotic Cell Division Machines.

(Core module. Duration: one week)

Cellular Design II: This module will build on Cellular Design I, developing concepts and applications from use in situations where engineering of single cells is undertaken to examples where impact is made at a multi-cellular level. Topics covered will include  Multicellular computing, Biofilms and mathematical modelling of microbial communities, Synchronisation/Quorum sensing and Synthetic communities.

(Advanced module. Duration: one week)

Biomimetic Construction II: This module will build on Biomimetic Construction I. After information regarding the rules for Biopolymer folding/ assembly are explained, these rules will be applied to the synthesis of DNA and RNA nanostructures and materials and developed further for more complex Peptide nanostructures and materials and even Enzymes and pathways. Finally, Antibodies and mimics, de novo proteins, natural motors, synthetic mimics will be discussed.

(Advanced module. Duration: one week)

Advanced Design I: This module will build on concepts discussed throughout the course. Lectures on Systems and Control, Retroactivity and Scalability, Noise and Stochasticity will build to describe how Synthetic Circuits can be built in mammalian cells and the insights we can garner from evolution regarding system design will be discussed. Delivery will be by conventional lectures, discussion sessions, reference to the literature and MATLAB/pen and paper exercises.

(Advanced module. Duration: one week

Advanced Design II: This module will re-evaluate the engineering mantra in the biological domain and its expansion to organisational levels beyond cellular circuits. In the former domain, the focus will be on the relation between evolutionary dynamics and engineering. In the latter domain, we will discuss engineering at the level of microbial communities, tissues, and plants. Delivery will be by conventional lectures, discussion sessions, reference to the literature and MATLAB/pen and paper exercises.

(Advanced module. Duration: one week)

ELSA/Responsible Research and Innovation: This module introduces the core concepts and approaches adopted in ethical, legal and social aspects (ELSA) of synthetic biology. It will enable students to reflect critically on their own and others assumptions about synthetic biology and to articulate the relevance of ELSA for the present and next stages of their careers. It is designed to give students a basis on which to discuss synthetic biology with a range of publics and to act as ambassadors for synthetic biology. Topics include ethics, justice, dual effect, the nature of ‘humanity’, public understanding of synthetic biology, biosecurity, synthetic biology as an interdisciplinary research community, futures, expectations and values.

(Core module. Duration: 4 days)

Wetlab: The Wet Lab course is designed to familiarise students with the practical techniques required for modern synthetic biology. One half of the course will concentrate on the basic molecular biology required to construct and characterise iGEM-style genetic circuits. Techniques from DNA assembly and cloning through to quantitative characterisation of parts using plate readers and fluorescence microscopy will be covered.

The other half of the course will cover experimental techniques for biomimetic construction: students will learn how to design, assemble and characterise structures and devices built from DNA.

 

(Core module. Duration: Tue-Thu afternoons of 2nd Term, except during project weeks.)