Exploring the Design Space of Stripe-Forming Networks
Event details
| Date | 18.05.2015 |
| Hour | 12:15 |
| Speaker | Yolanda Schaerli, Ph.D., University of Zurich (CH) |
| Location | |
| Category | Conferences - Seminars |
BIOENGINEERING SEMINAR
Abstract:
Gene regulation networks are essential for the processing of information that cells receive. To study the function and properties of gene regulatory networks synthetic biology is a promising tool. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. We went beyond individual networks and explored both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally tested every possible 3-node network for stripe formation in a morphogen gradient. We discovered four different dynamical mechanisms to form a stripe and identified the minimal network of each group. Next, with the help of newly established engineering criteria we built these four networks synthetically and showed that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allowed us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
Bio:
2014 - present SNSF Ambizione fellow, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
2012 - 2014 Marie Curie post-doctoral fellow, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
2011 – 2012 SNSF post-doctoral fellow, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
2007 - 2010 PhD researcher, Departments of Biochemistry and Chemistry, University of Cambridge, UK
2002 - 2006 MSc in Biochemistry and Molecular Biology, ETH Zurich, Switzerland
Abstract:
Gene regulation networks are essential for the processing of information that cells receive. To study the function and properties of gene regulatory networks synthetic biology is a promising tool. Gene circuits with predefined behaviours have been successfully built and modelled, but largely on a case-by-case basis. We went beyond individual networks and explored both computationally and synthetically the design space of possible dynamical mechanisms for 3-node stripe-forming networks. First, we computationally tested every possible 3-node network for stripe formation in a morphogen gradient. We discovered four different dynamical mechanisms to form a stripe and identified the minimal network of each group. Next, with the help of newly established engineering criteria we built these four networks synthetically and showed that they indeed operate with four fundamentally distinct mechanisms. Finally, this close match between theory and experiment allowed us to infer and subsequently build a 2-node network that represents the archetype of the explored design space.
Bio:
2014 - present SNSF Ambizione fellow, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Switzerland
2012 - 2014 Marie Curie post-doctoral fellow, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
2011 – 2012 SNSF post-doctoral fellow, EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Barcelona, Spain
2007 - 2010 PhD researcher, Departments of Biochemistry and Chemistry, University of Cambridge, UK
2002 - 2006 MSc in Biochemistry and Molecular Biology, ETH Zurich, Switzerland
Practical information
- Informed public
- Free