Meeting with Shireesh Srivastava
| Date | |
|---|---|
| Department | GeneralHP |
| Description | Discussion on modelling and feasibility |
| HP sub-branch | |
| Links/media | |
| Participants | |
| Property | |
| Property 1 | |
| Property 2 | |
| Type | Meetings |
Shireesh Srivastava: http://icgeb-bioenergy.org/shireesh-srivastava/
Post-meeting:
- 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
- UTEX2973 full-genome fluxome: http://www.plantphysiol.org/content/179/2/761
- 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
