Team:IISER-Pune-India/TeamNotebook/Team Notebook 11e9906b405543a29361e38a50c81024/Meeting with Indumathi (Ph D from Karthik's Lab II dd6c7dd713db4661b570e40ac856460e

Meeting with Indumathi (Ph.D. from Karthik's Lab IIT-M)

Meeting with Indumathi (Ph.D. from Karthik's Lab IIT-M)

DepartmentDry Lab
DescriptionMeeting with Indumathi (Dr Raman's PhD student) to figure out errors with UTEX model and further directions for dry lab work.
HP sub-branch
Property 1
Property 2

FBA Model of UTEX 2973

Problems with our model - The bacteria has a 0 growth rate

Potential reasons for this to happen (Our view):

  • Dead End Metabolites
  • Gaps

Potential reasons for this to happen (PhD view):

  • Objective function is wrong
  • No exchange reactions
  • No sink reactions
  • Rarely dead end metabolites

Possible solutions (PhD view):

  • Try checking for exchange reactions - tried and failed; most of the reactions are appropriately named in the UTEX 2973 model (700 reactions) and therefore exchange reactions are automatically identified.
  • Try adding sink reactions for all the metabolites that are secreted out - *Haven't tried yet
  • Check for carbon uptakes - found to be 0 but when you examine the model reaction by reaction you get to see there are uptakes and therefore this cannot be the solution.
  • Find a SBML model - found one for the other paper (PCC and UTEX combined) but the model had a field missing and therefore could not be used
  • Ask the authors of the paper for the model (700 rxns)

Community FBA and the Co Culture Bit


  • Won't assume same growth rates
  • Takes into consideration all possible interactions

You can rule out Network analysis because FBA is easier

Compare fluxes of individual models and community model to characterize the extra interactions in the coculture apart from monocultures.

Medium Optimisation

  • MAMBO algorithm - used to find minimal media required for an organism. This doesn't take care of environmental factors like wavelength and intensity of light n all (mostly used for monocultures afaik).
  • Medium optimisation from an already known starting point
    • Identify the media components in a medium used for this particular co culture
    • Notes down their concentrations (in FBA terms uptake rates)
    • Very few reactions will have high fluxes for media components, put those to zero and check if they're really very necessary for growth.
    • Keep changing values to find the best optimisation
    • The test it out in wet lab

Carbon Footprint

1^13C^3C labeling can be used to find how much carbon has been used by E. coli from the input CO2CO_2 in the reactor, and how much has been used from e.coli's own CO2CO_2 release.

Although this doesn't exactly give us what we want, this can be used as a striating point to develop an algorithm that is specific to our case.

Note : She seemed very interested in our project and we have asked her to be our PhD mentor, she said she will get back to us after discussing it with her guide.