BC2 Evolution and Genetic Engineering - Thinking like a Biologist

Description

Synthetic biology (SB) is a research field that combines the investigative nature of biology with the constructive nature of engineering, with the ambition to develop a veritable methodology with which to design and construct complex biological systems following general principles.

In practice, a Synthetic Biologist selects molecular elements from natural systems and uses them as modules to construct new networks to fulfill specific
desired goals. Thats why,the rise of this field required both, the advance of the genetic engineering tools and the re-understanding of cells as programmed information-processing entities whose functions are executed by the combination of individual functional modules. Most of the initial creations of synthetic biology had been directed towards the building of artificial computational devices using engineered biological units as basic building blocks.

In this course we will study some of the paradigmatic cellular computational devices, from the initial oscillator to the distributed computation of multicellular consortia. The synthetic constructs presented will serve to illustrate:

- How to translate our desired boolean function into a biological modular design. These designs can be inspired by, but need not mimic, the man-made electronic devices.

- The basics of genetic engineering techniques that allow us to create synthetic genetic modules that incorporate sensing and processing components, able to respond to specific inputs and produce outputs that act as inputs for other modules or trigger cellular responses. We will also learn the different levels where we can act to control the cellular information processing: DNA, RNA and proteins. Also, how to build our genetic construct by "evolution".

- To disscus about the challenges that we face to assemble more and more modular, customizable, scalable and complex systems, because although these modules function as predicted, stochastic fluctuations in gene expression levels and molecular cross talk significantly affects the ability to connect multiple of them to build a larger system in a single cell. In fact, unlike in electronics where all wires are made of the same material, in biological systems where substances share the same medium, each connection need to be performed by a different molecular element.

- To revise the unique features of biological living systems computation.

Objectives

Understanding the principles and challenges of Synthetic Biology, with enfasis on its application to biocomputation (logic circuits). All participants would get an overview of the basic and advanced technologies in genome and evolution engineering.

Literature

-Nurse, P. (2008). Life, logic and information. Nature, 454(7203), 424-426.
http://www.nature.com/nature/journal/v454/n7203/full/454424a.html

-Lim, W. A. (2010). Designing customized cell signalling circuits. Nature reviews Molecular cell biology, 11(6), 393-403.
http://www.nature.com/nrm/journal/v11/n6/full/nrm2904.html

-Kwok, R. (2010). Five hard truths for synthetic biology. Nature, 463:288–290.
http://www.nature.com/news/2010/100120/full/463288a.html

Course location

Günne

Course requirements

None

Instructor information.

Instructor's name

Nuria Conde-Pueyo

Email

cf. website

Vita

Núria Conde is post-doc at the Universitat Pompeu Fabra (Complex System Lab). She gathered a bachelor degree in Biology and a technical engineering degree in Computer science (both, at UPF). She has been working in a lab for almost 10 years and holds a PhD in Synthetic Biology and Biocomputation. She published around 10 papers in peer-reviewed journals.
Currently, is the CSO of a very new biotech startup company (Moirai Biodesign), dedicated to design RNA sensors for cancer diagnoatics and therapy. She is also an external Biology consultant for IAAC (Institut d'arquitectura avançada de Catalunya) and is lecturing several workshops at Green FabLab Barcelona, as local tutor of the MIT on-line curse HTGAA. Her commitment to bring science not only to students, but to society at large, motivated her to fund the Barcelona Biohack Space (http:\\www.diybcn.org), which she presides. She has presented works in museums, like for example the agar bioprinter at CCCB Human+ exhibition.

Website

https://www.researchgate.net/profile/Nuria_Conde-Pueyo/publications