Synthsys Event

Grzegorz Kudla (MRC Human Genetics Unit)
Empirical fitness landscape of yeast U3 snoRNA
Accurate mapping between genotype and phenotype is key for understanding the functions of genes at the molecular level. To evaluate the phenotypic consequences of all possible single and double mutations in a model gene, we constructed a synthetic library of more than 100,000 randomly mutated variants of the yeast gene U3, which encodes a noncoding small nucleolar RNA (snoRNA). We measured the fitness of yeast strains carrying these mutations by performing a competitive growth experiment of the entire pool of mutants followed by deep sequencing.
Victor de Lorenzo (National Center of Biotechnology CSIC)
Cyborg-ization of soil bacteria for smart degradation of environmental pollutants
Because of its adaptation to sites polluted with toxic chemicals, the soil bacterium Pseudomonas putida is naturally endowed with metabolic and stress-endurance qualities of considerable value for hosting energy-demanding and redox reactions implanted thereof. We have built on the growing knowledge of strain P. putida KT2440 for designing a derivative deleted of 11 non-adjacent genomic deletions, spanning 301 genes (4.3 % of the genome) for enhancing desirable traits and eliminating attributes which are detrimental in an expression host.

Seth Blackshaw (John Hopkins)

Systems Biology of Retinal Cell Specification

The mammalian central nervous system is made up of hundreds of distinct cell types.  However, the molecular mechanisms that specify this amazingly diverse population is poorly understood.  We use the mammalian retina as a model system to investigate this question, as it contains only seven major cell types, each of which differentiates during a discrete temporal window.  I will discuss how we use comprehensive gene expression profiling, in combination with in vivo electroporation, as a means of identifying an E3 SUMO ligase that controls photoreceptor identity.  Furthermore, I will describe how we have developed and used human proteome microarrays as tools for global identification of SUMO-modified and SUMO binding proteins, and as a means of isolating ultraspecific monoclonal antibodies to key human developmental regulatory factors.


Professor Stephen long FRS

27th June 2014, 12noon

The Centre for Systems and Synthetic Biology (SynthSys) at the University of Edinburgh is delighted to be hosting Stephen Long, who will speak on ‘Computationally guided systems and synthetic biology approaches to increasing photosynthetic efficiency in crops’

Dan Stanzione, Director and Matthew Vaughn, Director of Life Sciences
Texas Advanced Computing Center, The University of Texas at Austin
Title: The iPlant Collaborative: Cyberinfrastructure for 21st Century Biology

iPlant is a new kind of virtual organization, a cyberinfrastructure (CI) collaborative created to catalyze progress in computationally-based discovery in plant biology. iPlant has created a comprehensive and widely used CI, driven by community needs, and adopted by a number of large-scale informatics Projects and thousands of individual users. iPlant holds more than 1.5 petabytes of user data comprising several hundred million files today, and is thus deeply

25th June

James Osborne (Oxford/MSR Cambridge)
Title: Multiscale modelling of multicellular biological systems: mechanics, development and disease

‘Uncovering the hidden half of plant biology using systems approaches’

Prof Malcolm Bennett

Centre for Plant Integrative Biology (CIPB), University of Nottingham
12noon, Lecture Theatre G10, Darwin Building
Host:  Andrew Millar

Talks by -

Stewart Mitchell- Business Development Manager, IBioIC (Scottish Industrial Biotechnology Innovation Centre)
'Challenges faced by IBioIC industry members and their areas of interest for IB projects'
Gabriela Toledo-Ortiz
A regulatory module coordinating light and temperature control of photosynthetic gene transcription

9.30am-10.30am, Waddington 1.08

Johnathan A. Napier
Department of Biological Chemistry and Crop Protection, Rothamsted Research

Heterologous synthesis of omega-3 long chain polyunsaturated fatty acids in transgenic plants via iterative metabolic engineering: a terrestrial source of fish oils

Talks by -

Julien Michel (Chemistry) – Computational approaches to quantify and engineer protein-ligand interactions

Vincent Danos (Informatics) - The DARPA Big Mechanism project:


9.30am - 10.30am

Waddington 1.08