Team:IISER-Pune-India/TeamNotebook/Team Notebook 11e9906b405543a29361e38a50c81024/Meeting with Shireesh Srivastava eca7e151929f4ec7b34004a10dc0104d

Meeting with Shireesh Srivastava

Meeting with Shireesh Srivastava

DescriptionDiscussion on modelling and feasibility
HP sub-branch
Property 1
Property 2

Shireesh Srivastava:


  • Talk to Prem - design constructs with our PhD mentors, mail her to contact the sucrose/Viral guy in PhD, and people who're working with modelling in their lab
  • Mail Shireesh for FBA papers, PhD students
  • Syed Shams Yazdani at ICGEB works on metabolic engineering, we can contact him for that

Meeting Summary:

  • Equipment required: Lighted incubator; For engineering - Restriction enzymes, a way to measure sucrose
  • pH: cyanobacteria grow better in basic pH, because their primary import mechanism is bicarbonate transporter
    • might want to have a slightly basic pH (7 - 7.5), as in the case of co-cultures the rate of the slower organism must be preferred, Zhang (2020) - pH =8.3
  • Light intensity: needs to be measured and controlled
    • For certain Synechococcus that might be fairly high, might have to measure wavelength too
  • Temperature: don't have to worry too much, as they both grow at similar temperatures (35-38C, Zhang (2020) = 30C)
  • Monitoring CO2 concentration and light for optimisation: Bubbling in CO2 in a real simulation would get complicated because of self-shading (???)
    • Can instead look at Flux Balance Analysis: as a starting point, vary the parameters in the physiological range
  • Doing wet lab would be the major challenge here - simulation might not be able to produce the results that actual wet lab can
  • Population dynamics: for a typical system, when you produce something, you take an average of the population for yield
    • Will be hard to practically implement, might want to look at FBA instead
  • Can set up a bioreactor and procure restriction enzymes and primers, begin culturing the cells, will however require time
  • ICGEB is shut down to external trainees, might be more positive in a month
    • They currently work with PCC 7002 and BDU 130
    • Is ok letting us work there as long as we can procure strains from Wangikar's lab
  • Wet lab: What we can do while waiting for labs to open is
    • prepare constructs
    • design experiments
    • order primers
    • procure money for the following
  • Dry lab: population dynamics may not be the way to go with this
    • He does do FBA, challenge is how to get it executed, he can give us remote access to FBA work
    • Can set up meeting with his students and provide remote access to their simulations
  • Growing E. coli in salt stress: we can adapt the E. coli to the salt stress (his lab also does that)
  • Self-shading: self-shading problems would depend on the scale of your project
    • has been modelled before
  • Promoters: IPTG very leaky, use native promotors instead
    • cpcb560 promoter with very high expression in presence of light
  • CO2 modelling: it's been reported that higher co2 would be better, so ideally you would bubble in co2, optimal levels known to be 1-5%
  • Phosphate and Nitrate: Might be limiting, measure rate of intake by the coculture, can be added periodically
  • Aquarium bubbler or gas exchanger needed to aerate culture