Iraes Rabbers / PhD student

IR_squareBackground and current projects

I am a PhD student in the group of prof. dr. Frank Bruggeman, as part of the Systems Bioinformatics group of the Teusink lab. At the VU, I obtained my bachelor in Biology in 2009 and my master in Biomolecular Sciences in 2012, with specializations in Systems Biology and Cell Biology.

I am currently working on the VIDI project of Bruggeman that focusses on the link between molecular interactions and evolutionary fitness using E. coli as a model organism. As the specific growth rate (i.e. fitness) of a microorganism depends on the identity and level of expressed proteins, it is important for cells to balance the costs and benefits of protein production (see for example Berkhout et al, Genetics, 2013). In this project, we will explore several aspects of this phenomenon: How does fitness depend on costs and benefits of proteins? Does the optimal expression level vary across environments? Is wildtype E. coli always able to reach this optimal level?

In addition I am working on experimental evolution of high yield phenotypes of L. lactis and E. coli, through the use of a novel emulsion culturing method developed by Bachmann et al (PNAS, 2013). What metabolic changes lead to an increase in biomass yield? And which mutations underlie these changes? Does the yield/rate trade-off exist?

Through a combination of modeling and experiments, we hope to shed new light on these questions.

Overview_IRexperiments


Conference talks

  • MEB International Conference on Metabolic Engineering in Bacteria (2015) Amsterdam, The Netherlands
  • SMBE Society for Molecular Biology&Evolution Meeting 2015 (2015) Vienna, Austria
  • ESEB European Society for Evolutionary Biology Meeting 2015 (2015) Lausanne, Switzerland
  • NBC-16 Biotechnology the next level (2016) Wageningen, The Netherlands

 

Attended conferences and courses

  • SB@NL (2013)
  • International Conference on Systems Biology ICSB Copenhagen (2013)
  • Kluyver Centre symposium on Putting Microbial Genomes to Work (2013)
  • Advanced Lecture Course on Systems Biology Innsbruck (2014) Poster presentation
  • Wageningen University, WCSB symposium on Systems Biology for Food, Feed, and Health (2014) Poster presentation
  • Lyon SysBio (2014) Poster presentation
  • KNVM fall meeting on Microbial Biotechnology (2014)
  • SB@NL (2014) Poster presentation
  • BioSB (2015) 3rd prize in poster competition
  • KNVM fall meeting on Microbial Biotechnology (2015) top 5 poster, selected for poster pitch
  • Advanced Lecture Course on Systems Biology Innsbruck (2016) Poster presentation

 


Publications

  1. Rabbers, I, van Heerden, JH, Nordholt, N, Bachmann, H, Teusink, B, Bruggeman, FJ et al.. Metabolism at evolutionary optimal States. Metabolites. 2015;5 (2):311-43. doi: 10.3390/metabo5020311. PubMed PMID:26042723 PubMed Central PMC4495375.
  2. Bachmann, H, Fischlechner, M, Rabbers, I, Barfa, N, Branco dos Santos, F, Molenaar, D et al.. Availability of public goods shapes the evolution of competing metabolic strategies. Proc. Natl. Acad. Sci. U.S.A. 2013;110 (35):14302-7. doi: 10.1073/pnas.1308523110. PubMed PMID:23940318 PubMed Central PMC3761572.
Search PubMed

 


Supervision of students

NameBSc./MSc.PeriodSubject
Tim van WagensveldBSc.March 2013 - June 2013Experimental evolution of increased efficiency through serial propagation in emulsion
Marit Hoffmeyer (together with Anne Schwabe)MSc.August 2013 - December 2013Does E. coli express its H+-ATPase to an optimal level?
Wouter W. WoudMSc.September 2013 - March 2014Experimental evolution of increased efficiency through serial propagation in emulsion
Rebeca AlbaBSc.January 2014 - June 2014Does E. coli express its H+-ATPase to an optimal level?
Emmeline Malari (together with Anne Schwabe)BSc.March 2014 - June 2014Why is the electron transport chain of E. coli branched?
Mirella KalafatiMSc.August 2014 - December 2014Construction of a promoter library in E. coli
Azize BuyukBSc.October 2014 - May 2015Does E. coli express its H+-ATPase to an optimal level?

 

Supervision of practicals in courses

  • Building Blocks of Life (Bouwstenen van het leven)
  • Research in the Biomedical Sciences 2 (Onderzoek in de Biomedische Wetenschappen 2)
  • Mathematics module of Introduction to Systems Biology
  • The Microbial Cell (De Microbiële Cel)
  • Molecular Microbiology

 


Contact information

Email: i.rabbers[at]vu[dot]nl

Systems Bioinformatics
Vrije Universiteit Amsterdam
room O|2 01W57
De Boelelaan 1108
1081 HZ Amsterdam
Tel: 020-5982705