Synthsys Event

Uwe Ohler
(Professor, Systems Biology of Gene Regulation, Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Department of Biology, Humboldt University)
Host: Guido Sanguinetti

Time: 12noon
Location: C.H Waddington Seminar room 1.08, King's Buildings Campus

Bert Poolman (Dept of Biochemistry, University of Groningen)

Bacterial cell volume regulation and traffic & translocation in crowded environments

Cell volume regulation is crucial for any living cell because changes in volume determine the metabolic activity through e.g. changes in ionic strength, pH, macromolecular crowding and membrane tension. These physical chemical parameters influence interaction rates and affinities of biomolecules, folding rates, and fold stabilities in vivo. Understanding of the underlying volume regulatory mechanisms has immediate application in biotechnology and health, yet these factors are generally ignored in systems analyses of cellular


Andrzej M. Kierzek (Professor of Systems Biology, University of Surrey)
‘Computer simulation of molecular cell biology’
Host: Peter Ghazal (
Short biography:
Professor Kierzek has over 15 years of experience in computational biology.  His research goal is to predict the dynamic behaviour of the living cell by computer simulation of the genome scale network models representing experimental data on interaction between molecules.
SynthSys Mini- Symposium
9.30am – 1.30pm
C.H Waddington Seminar room 1.08
9:30 – 10:00                Coffee & Pastries
10:00 - 11:00               John Heap (Imperial College London) 
                                      ‘Diverse hosts for applied synthetic biology’                                
Short talks
11:00 - 11:15               Louise Horsfall (SynthSys, Biological Sciences)
11:15 - 11:30               Martin Wear (Biological Sciences)
11:30 – 11.50              iGEM team
11:50 - 12:30               Lunch break    
12:30 - 13:30               Peter Burkhard (University of Connecticut)
                                      ‘Design of protein nanoparticles with built-in adjuvant properties as vaccines for malaria or nicotine addiction’
Jackie Vogel
(Associate Professor of Biology, McGill-Canadian Pacific Professor)
"Investigating the dynamic properties of complex molecular machines in vivo and in silico"
The mitotic spindle is a complex molecular machine that functions to accurately segregate genetic material between mother and daughter cells. Prior to mitosis, this machine undergoes major changes in its structure and behavior, first by forming a bipolar spindle and subsequently breaking symmetry of the two poles. Both are required for anaphase. In this seminar, I will first describe our analysis of the physical basis of the initial step of pole separation to form the spindle and facilitate chromosome capture, and conclude with our study of the process of symmetry breaking required to position the spindle at the future plane of cytokinesis prior to anaphase.
Suwan Jayasinghe (Centre for Stem Cells and Regenerative Medicine & Mechanical Engineering, UCL)
Biospray approaches for regenerative biology/medicine and therapeutics
The ability to manipulate and distribute living mammalian cells with control presents fascinating possibilities for a plethora of applications in our healthcare. These imply several possibilities in tissue engineering and regenerative biology/medicine, to those of a therapeutic nature. The physical sciences are increasingly playing a pivotal role in this endeavour by both advancing existing cell engineering technology and pioneering new protocols for the creation of biologically viable structures. The talk will introduce the leading technologies, which have been fully validated from a physical, chemical and biological stand point for completely demonstrating their inertness for directly handling the most intricate advanced material known to humankind.

Dr. Davide Cammarano (James Hutton Institute, Invergowrie, Dundee)

“The Babel’s tower of modelling: Is it possible for crop, cell, and molecular modellers to speak the same language?”

Crop simulation models integrate the temporal and multiple interaction of stress on crop growth each day under different environmental and management conditions. They are used in many research areas and for different purposes; researchers can use them to extrapolate data beyond field experimentation. The aim of this seminar is to show how crop simulation models are used  as a tool for understanding the crop’s temporal and spatial variability within fields, and how farmers can use their outputs in making decisions for the season. And, their use in climate change impact studies.

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.