Modelling and Microbiology – Conference at the eScience Institute

Tomorrow is the final meeting at the eScience Institute in Edinburgh: our conference on Modelling and Microbiology. Although I am a co-organizer, I am unable to attend for family reasons. We will be ably represented by Dorota Herman, who will be speaking on Tuesday at 3:05pm.

The entire meeting will be webcast and can be watched here. We have many good speakers, so I am posting the full speaker timetable below.

Monday July 4th

1.45-2 Welcome (Rosalind Allen)

2-3 Robert Austin (Princeton)
Darwin, ecology and the emergence of bacterial resistance: an
attempt at a synthesis

3.30-4.15 Martin Howard (John Innes Centre)
Dissecting the dynamics of low copy number plasmid segregation

4.15–5 Tobias Bollenbach (IST Austria)
Microbial responses to antibiotic combinations

Tuesday July 5th

9.30-10.30 Martin Ackermann (ETH Zuerich)
An evolutionary perspective on phenotypic heterogeneity in bacteria

11-11.45 Peter Lund (Birmingham)
Insights into stress response from laboratory-based evolution

11.45-12.05 Sara Mitri (Oxford)
Social evolution in microbial communities

12.05-12.25 Fatima Drubi (Leiden University)
Do bacteria sporulate as a bet-hedging strategy in stochastic
environments?

2-2.45 Alexander Morozov (Edinburgh)
Self-assembled bacterial rotors

2.45-3.05 Bartlomiej Waclaw (Edinburgh)
Simple models for bacterial evolution with migration

3.05-3.25 Dorota Herman (Birmingham)
Mathematical model for transcriptional regulation of RK2 plasmids and
its evolutional optimisation

3.55-4.40 Jan Kreft (Birmingham)
Individual-based modelling of horizontal gene transfer in chemostats
and biofilms

4.40-5.15 Phil Aldridge (Newcastle)

Continuous control of flagellar gene expression by the s28-FlgM
regulatory circuit in Salmonella enterica

Wednesday July 6th

9.30-10.30 Oskar Hallatschek (MPI Goettingen)
Genetic drift and selection in growing biofilms

11-11.45 Ian Stansfield (Aberdeen)
Negative feedback loops in the translational control of gene
expression

11.45-12.05 Leena Nieminen (Strathclyde)
Modelling metabolic switching in differentiating bacterium
Streptomyces coelicor

12.05-12.25 David Richards (John Innes)
The mechanistic basis of hyphal branching in Streptomyces

2-2.45 Mamen Romano (Aberdeen)
The dynamics of demand and supply in mRNA translation

2.45-3.05 Dominique Chu (Kent)
Optimisation of gene expression resources in bioprocessing host cell
lines

Thursday July 7th

9.30-10.30 John Little (U. Arizona)
Stochastic modelling of the phage lambda regulatory circuit: prophage
induction and stability

11.00-11.45 Francesco Falciani (Birmingham)
A systems biology approach sheds new light on bacterial acid
resistance

11.45-12.30 Kevin Foster (Oxford)
Spatiogenetic structure and cooperation in microbe

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e – Science Institute Theme 14 Workshop: Microbiology Modelling and Evolution

In the last three days I have been running a focussed workshop at the e-Science Institute in Edinburgh on microbiology modelling and evolution. With 16 contributors roughly equally split between experimentalists and modelers, we presented and discussed scientific work at the interface between experimental and modelling approaches to evolution in microbiology.

At the start of the meeting, I set out my personal views on the challenges and opportunities at this interface – my hope was that at the end of the meeting my views would be in need of updating ! From a biological perspective, the challenges are around emergence of antimicrobial resistance and pathogenicity; the opportunities afforded by fast and cheap genome sequencing. From a modelling perspective, the challenges are around developing suitably realistic models, of generating experimentally testable hypotheses, and of gaining recognition of evolutionary computing as a means to test hypothesis; the opportunities are afforded by the capacity for long-term evolution by high performance computation.

Every talk was interesting and of a high standard – and the discussion was lively and engaging. A few points that came up that I found especially salient were: (i) microbes are not just interesting/important in themselves, but also as models for general biological processes, especially social processes, including host-pathogen interactions, evolution of cooperativity and evolution of communication. (ii) The challenge of genomic diversity is greater than I even imagined. I’m already used to genomic diversity in E. coli strains, but it was amazing to see it across so many bacteria studied, including Pseudomonas aeruginosa from a single patient’s lung, or Rhizobium from root nodules in clover and vetch in a single tiny patch. (iii) The importance of considering horizontal gene transfer, and thus different levels of selection, in models of mircobial evolution. (iv) The criticality of spatial organization in both real and simulated evolution, and thus the opportunity to use high performance computation for simulation of spatial scales as well as time scales.

I was heartened by the genuine sense of good will to work together at this interface, and a shared view that ‘Systems Biology’ needs to move beyond modelling how systems are now, into being able to explain why systems might have evolved to be the way they are, and predict how they might evolve.

e-Science Institute Theme 14 starts today

Today saw the start of Theme 14 – Modelling and Microbiology – at the e-Science Institute in Edinburgh. The theme will run for 12 months and covers the interface between high performance computation and microbiology. We will bring together mathematicians, physicists, computer scientists and microbiologists in a series of focused workshops followed by a larger research conference next summer. The topics covered are:

  • Stochasticisty and microbial infection (this week)
  • Experiments and simulations of evolution
  • Modelling of metabolism

The next two workshops will be held in January and April and the conference at the end of June.

The theme has been funded by the e-Science Institute and is a collaboration between Rosalind Allen, Jamie Wood and myself.

The opening lecture (by Ros) will be webcast and I will post a link when it becomes available.