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My work focuses on the ecology and evolution of viruses and bacteria. I am particularly interested in the evolution of genome organization and its implications for adaptation, and the effects of size and structure of populations on adaptation and the repeatability of evolution. I work on a broad range of topics, ranging from understanding the exotic genome organization of some plant viruses (multipartite viruses), to how the community-context and spatial processes influence the evolution of antibiotic resistance in bacteria, to developing and testing simple models of bacterial and virus infection. I'm participating in the eco-evolutionary dynamics, disease ecology and microbiomes NIOO research themes.

 

Short bio

I've been fascinated by living organisms and scientific exploration for as long as I can remember. My interest in evolution was first sparked at an early age by exposure to Creationist materials, so Kent Hovind does get some credit for making an evolutionary biologist out of me. Later on I became particularly interested in viruses, and pounced on the opportunity to do a PhD on the evolution of baculoviruses infecting caterpillars. Afterwards I worked on the evolution of plant RNA viruses, trying to understand the evolution of their large-scale genome organization (genome size, gene order) by means of experimental evolution. More recently I've worked on an entirely different bug - an antibiotic resistance gene (TEM beta-lactamase) in Escherichia coli - and different questions - how repeatable and predictable is the evolution of antibiotic resistance? In 2017 I had the privilege of joining the Microbial Ecology Department at NIOO-KNAW as a tenure track researcher. I'm interested in whisky, korfbal, music (currently I am mastering the kazoo), the occasional spat of drawing, and did I mention modeling bacterial and viral infection?

 

 

Work experience:

2017-present: Tenure-track researcher in the Microbial Ecology Department, NIOO-KNAW.

2014-2017: Postdoctoral researcher at Institute of Theoretical Physics, University of Cologne & the Laboratory of Genetics, Wageningen University and Research

2012-2014: Juan de la Cierva postdoctoral fellow at the Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain

2010-2012: NWO Rubicon postdoctoral fellow at the Instituto de Biología Molecular y Celular de Plantas (IBMCP, CSIC-UPV), Valencia, Spain

2008-2009: Postdoctoral researcher at the Quantitative Veterinary Epidemiology Group, Wageningen University and Research

 

Education:

PhD (2008): Infection biology and evolution of insect virueses, Laboratories of Virology and Genetics, Wageningen University and Research

MSc (2003): Life Sciences, Utrecht University

BSc (2001): Science, University College Utrecht

 

Projects:

NWO VIDI Innovational Research Incentives Scheme (2017-2022): On the evolution of genome segmentation in plant RNA viruses

NWO/ZonMw Antimicrobial Resistance Program (2016-2020): Microbiome invasion and transmission of plasmid-mediated antimicrobial resistance (MITAR, Lead investigator: Dr. Egil Fischer.)

John Templeton Foundation ´Big Questions´ Program (2012-2015) :Experimental evolution of genome architecture and complexity in an RNA virus (Lead investigator: Dr. Santiago F. Elena)

Juan de la Cierva personal fellowship (2012-2014)

NWO Rubicon personal fellowship (2010-2012)

 

Formal supervision of PhD students:

Bui Thi Minh Dieu (2010)

Tran Thi Tuyet Hoa (2012)

Anouk Willemsen (2016)

Jesse Alderliesten (expected 2021)

 

 

Video

NWO VIDI 2016

Project Summary

Genome segmentation, the division of the hereditary material into multiple physical units, is widespread across all domains of life. Although many viruses also have segmented genomes, some viruses go a step further and package each segment into a different virus particle. The separate packaging of each genome segment imposes a massive cost, because all virus genome segments must enter the same cell to cause infection. The benefits of multipartition are poorly understood, and it is therefore a mystery how multipartite viruses can thrive. Recent work has shown that frequency of the different types of viral particles can change over time, and that it converges on an equilibrium. The virus particles containing different genome segments are then present at different frequencies, and some observations suggest these changes might be adaptive. Moreover, this equilibrium is different for alternative host species, suggesting that multipartition might also have evolved to regulate gene expression in different environments. Here, we will test the hypothesis that multipartition has evolved to regulate gene expression in a robust yet flexible manner, using a multidisciplinary approach including mathematical modeling, laboratory experiments and ecological fieldwork. Models will be used to predict the robustness and the existence of multiple genome segment frequency equilibria. Experimental evolution will be used to test whether the genome segment frequency equilibrium changes under different environmental conditions. Experiments will also be performed to test how changes in genome segment frequency affect the expression of viral proteins. Finally, fieldwork will be performed to measure genome segment frequencies in the natural virus populations. Knowledge utilization will focus on a two-way interaction with plant inspection services, seed producers and biotechnology companies, to develop more effective ways to monitor multipartite viruses and better approaches for engineering resistance against viruses in plants.

 

 

NWO ZonMW Antibiotica Resistentie 2016: Microbiome Invasion and Transmission of plasmid-mediated Antimicrobial Resistance (MITAR)

 

 

Project Summary

Plasmid-mediated antimicrobial resistance (pAMR) occurs in both humans and animals and requires One-health solutions, which include a holistic approach integrating veterinary, medical and environmental disciplines. Reduction of antimicrobial usage is one of the measures against further proliferation of pAMR. The prevalence of pAMR in poultry remains, however, high after reductions in antimicrobial usage, and new forms of pAMR arise (e.g. mcr-1). In humans, a parallel problem occurs rendering pathogens multi-resistant. Currently we are not able to assess the risk of new pAMR to invade the microbiome of an individual (human or animal) and whether it can be maintained within the microbiomes of a population of individuals. Understanding the key features of the microbiome determining the potential for invasion, colonization and evolution of pAMR is essential to lower the barriers for new innovative interventions. Principal Investigator: Dr. Egil Fischer (Department of Farm Animal Health, Utrecht University). Collaborators: Prof. Dr. Arjan Stegeman (Department of Farm Animal Health, Utrecht University), Prof. Dr. Arjan de Visser (Laboratory of Genetics, Wageningen University and Research).

 

Infection kinetics of viruses

  1. Zwart MP & Elena SF (2015) Matters of size: Genetic bottlenecks in virus infection and their potential impact on virus evolution. Annual Review of Virology 2: 161-179.
  2. Tromas N, Zwart MP, Lafforgue G & Elena SF (2014) Within-host spatiotemporal dynamics of plant virus infection at the cellular level. PLOS Genetics 10: e1004186.
  3. Lafforgue G, Tromas N, Elena SF & Zwart MP (2012) Dynamics of potyvirus systemic infection establishment: Independent yet cumulative action of primary infection sites. Journal of Virology 86: 12912-12922.
  4. Zwart MP, Daròs JA, & Elena SF (2011) One is enough: In vivo effective population size is dose-dependent for a plant RNA virus. PLOS Pathogens 7: e1002122.
  5. Werf W van der, Hemerik L, Vlak JM & Zwart MP (2011) Heterogeneous host susceptibility enhances prevalence of mixed-genotype micro-parasite infections. PLOS Computational Biology 7: e1002097.
  6. Zwart MP, Hemerik L, Cory JS, de Visser JAGM, Bianchi FFJA, van Oers MM, Vlak JM, Hoekstra RF & van der Werf W (2009) An experimental test of the independent action hypothesis in virus-insect pathosystems. Proceedings of the Royal Society B-Biological Sciences 276: 2233-2242.

 

Plant virus evolution

  1. Willemsen A, Zwart MP, Tromas N, Majer E, Daròs JA & Elena SF (2016) Multiple barriers to the evolution of alternative gene orders in a plant RNA virus. Genetics 202: 1503–1521.
  2. Willemsen A, Zwart MP, Higueras P, Sardanyés J & Elena SF (2016) Predicting the stability of homologous gene duplications in a plant RNA virus. Genome Biology and Evolution 8: 3065-3082.
  3. Cuevas JM, Willemsen A, Hillung J, Zwart MP & Elena SF (2015) Molecular adaptation dynamics of an RNA virus at different space-time levels. Molecular Biology and Evolution 32: 1132-1147.
  4. Zwart MP, Willemsen A, Daròs JA & Elena SF (2014) Experimental evolution of pseudogenization and gene loss in viral genomes. Molecular Biology and Evolution 31: 121-134.

 

Multipartite plant virus infection and evolution

  1. Wu B, Zwart MP, Sánchez-Navarro JA & Elena SF. (2017) Within-host evolution of segments ratio for the tripartite genome of Alfalfa mosaic virus. Scientific Reports 7: 5004.
  2. Sánchez-Navarro JA*, Zwart MP* & Elena SF (2013) Effects of the number of genome segments on primary and systemic infection for a multipartite plant RNA virus. Journal of Virology 87: 10805-10815.

 

Population size and the repeatability of the evolution of antibiotic resistance

  1. Salverda MLM, Komen J, Koopmanschap B, Zwart MP & de Visser JAGM (2017) Adaptive benefits of small populations on a rugged fitness landscape. Proceedings of the National Academy of Sciences U.S.A. 114: 12773-12778.
  2. Dijk T van, Hwang S, Krug J, de Visser JAGM & Zwart MP (2017) Mutation supply and the repeatability of selection for antibiotic resistance. Physical Biology 14: 055005.