Quantifying plasmid conjugation just got easier! This app is designed to make the estimation and reporting of plasmid conjugation rates from liquid mating cultures easier, more accurate, and more comparable. All data analysis functionality can also be found in the accompanying R package, and the methods are described in more detail in the preprint.
The tab Analyse experimental data allows you to upload your own data from liquid culture mating experiments and compute the corresponding plasmid conjugation rates. The two recommended methods to estimate these rates are the Simonsen end-point formula (Simonsen et al, J.Gen. Microbiol, 1990), applicable if all strains involved in conjugation grow at the same rate, and the ASM end-point formula, which relaxes this assumption (Huisman et al, 2020).
Both of these formulae will cease to be accurate once either the contribution of transconjugants to the overall conjugation becomes substantial, or the recipient dynamics are dominated by conjugation rather than growth. Based on the relative timing of these events, we derived the critical time within which the conjugation rate estimates remain valid.
The tab Simulate population dynamics allows users to simulate bacterial population dynamics under different models. We currently support the following models:
This app was created by Jana S. Huisman, in collaboration with Fabienne Benz, Sarah J.N. Duxbury, J. Arjan G.M. de Visser, Alex R. Hall, Egil A.J. Fischer, and Sebastian Bonhoeffer.
For questions or suggestions concerning the app and the implemented methods please contact:
jana.huisman [at] env.ethz.ch .
If you notice any bugs, or have trouble operating the app, please file an issue here, or also write to this email-address.
If the conjugator app or R package helped you in your work, please cite the manuscript:
Jana S. Huisman, Fabienne Benz, Sarah J.N. Duxbury, J. Arjan G.M. de Visser, Alex R. Hall, Egil A.J. Fischer, Sebastian Bonhoeffer. Estimating the rate of plasmid transfer in liquid mating cultures. BioRxiv 2020.
Here you can analyse experimental data from plasmid conjugation experiments and compute the corresponding conjugation rates.
Once you upload data under the “DRT” tab, you will be able to select which conjugation rate estimates to calculate. We recommended using the Simonsen end-point formula (“SM”), if all strains involved in conjugation grow at the same rate, and the ASM end-point formula (“ASM”), if this is not the case. The other methods are heuristics, which require less information on the growth rate of individual strains but are also more prone to biases. Mouse over the “i” next to each estimate’s name to get information on the required columns in the experimental data frame.
These methods to estimate conjugation rates will generally cease to be accurate once the experiment is measured past the minimal critical time. At that time either the contribution of transconjugants to the overall conjugation has become substantial, or the recipient dynamics are dominated by conjugation rather than growth. We provide estimates of the critical time to help determine whether the measured conjugation rate estimates are to be trusted. In general the calculation of the critical time requires an estimate of the transconjugant to recipient conjugation rate \(\gamma_T\), measured in a separate TRT experiment (for more information see Huisman et al., 2020). However, even if this data is not provided, we show how the critical times are expected to vary as a function of the ratio between \(\gamma_D\) and \(\gamma_T\).
To estimate all critical times, please upload data for the TRT experiment.
Prediction of the minimal critical time based only on the data of the DRT experiment.
On this page one can simulate the dynamics of three bacterial populations: donors \((D)\), recipients \((R)\) and transconjugants \((T)\). The populations compete for the same resources \((C)\), as they grow with growth rates \((\psi_{D/R/T})\). Donors conjugate with recipients at rate \(\gamma_D\), and transconjugants conjugate with recipients with rate \(\gamma_T\). Each time the parameters are changed (using the sliders), or a new model is selected, the dynamics are simulated anew.
Three population dynamic models can be selected:
The left plot shows the population dynamics of \(D, R\) and \(T\). The right plot compares estimates of the conjugation rate, assuming populations would be sampled at that point in time and the growth rates are known. Initially selected are \(\gamma_{max}\) from the Simonsen end-point formula and \(\gamma_{Dmax}\) based on the ASM end-point method. Dashed lines indicate the actual values of \(\gamma_D\) and \(\gamma_T\) (selected with the input sliders).
The critical times \(t_{c1}, t_{c2}, t_{c3}\) indicate the time points at which the assumptions underlying the ASM cease to be valid. To get an accurate estimate of the conjugation rate, one should ideally measure the mating populations before the minimal critical time. These critical times can be toggled on and off with the ‘Display critical times’ button. The end of the simulation is given by the ‘measurement time’.