Sultan Nazir

About Sultan

I am a doctoral candidate (since November 2023) in the Department of Theoretical Biology at Utrecht University, The Netherlands. My research focuses on horizontal gene transfer in structured microbial populations, with a particular emphasis on prophage-encoded pathogenicity. More broadly, I use mathematical and computational models to explore the fundamental principles shaping evolution. Alongside this, I maintain a strong interest in microbiology and invertebrate biology (the latter still on my to-explore list).

My PhD is supervised by Bram van Dijk. In our research group, we run "virtual experiments" to study the evolution of complex biological systems. Part of my doctoral research is in collaboration with Ben Ashby at Simon Fraser University, supported by the Swaantje Mondt Fund for complexity research. I also contribute to teaching and supervision at the bachelor’s and master’s level in Theoretical and Computational Biology.

Before my PhD, I completed an integrated BS-MS degree at the Indian Institute of Science Education and Research (IISER), Pune, with training in both Biology and Mathematics. My master’s thesis was carried out under the supervision of Brian Ingalls in the Department of Applied Mathematics at the University of Waterloo, Canada.

Projects

Spatial structure and the emergence of accessory genes on inducible prophages

Prophages are viral DNA commonly found embedded within prokaryotic genomes. These are generally costly to the prokaryotes due to their tendency to be induced. Upon induction, they kill the host cells and release phage particles that then infect other cells. However, prophages sometimes carry accessory genes. These are genes that offer some adaptations to the prokaryote but is not essential for cellular functions. Accessory genes are commonly found on Mogile Genetic Elements (MGEs) like plasmids and phages but phages seem inclined to carry virulence genes. While much research has been done to find why MGEs evolve to carry accessory genes, little is known in the context of phages.

Using Differential Equations and Individual-based models, we found some phage-specific mechanisms that can favour stable evolutionary transition of accessory genes onto inducible prophages. (1) If prophage induction rate is higher within an environment where the gene is selected for there is a positive selection pressure for mobility of the gene. (2) When selection occurs at a local scale in a spatially structured cell population, gene dispersal via phage particles help reinforce selection and hence creates a selection pressure for mobility.

See our preprint for more information:

Viral lifecycle dynamics and spatial structure explain why pathogenicity is prophage-encoded; Sultan Nazir, Bram van Dijk; bioRxiv 2025; Link to the preprint

Callibrating PDE models against time-lapse microscopy data

In this project, I aimed to bridge the gap between empirical and theoretical research in microbial spatial ecology. Growth of large bacterial communities can be described using Partial Differential Equations (PDEs). We developed a simple model to describe the growth of a bacterial colony on a 2-dimensional surface with growth-induced range expansion. Using an agarose pad, we then grew bacterial colonies and observed their growth using time-lapse microscopy.

Using an earlier developed pipeline, I callibrated our model against the microscopy data. I used a Simulated annealing protocol to fit the PDE model. Using the estimated parameters, we predicted the qualitative spatial dynamics for a more complex synthetic bacterial community using an extend PDE model and fluorescence microscopy.

You can find more information in my MS thesis: A growth-induced dispersal model of non-motile cells calibrated against time-lapse microscopy

Contact

If you have any feedback on my research or wish to discuss a potential collaboration, please feel free to drop me an e-mail at sultan.eeb@gmail.com or s.a.nazir@uu.nl.

We can also connect on Bsky @sultannazir.bsky.social.

Elements

i = 0;

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    print 'Iteration ' + i;
    deck.shuffle();
    i++;
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print 'It took ' + i + ' iterations to sort the deck.';