Week 1 HW: Final Project Ideas

Final Project Ideas

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Question 1. What would you like to biomanufacture and why?

Answer

Well, have a few ideas I would have to flesh out, but first I would like to build on my final project idea from How to Grow Almost Anything in the Spring (HTGAA). The idea is based around a low-cost paper-based biosensor kit for detecting mining pollutants, with lead(Pb), mercury (Hg), arsenic (As), and cadmium (Cd) being the target metals. The biosensor strip will have four spatially separated zones. Each zone would contain a freeze-dried reaction that responds to one of the target metals and produces a visible colour change when a drop of water rehydrates it.

Target MetalColor Output
Lead (Pb)Magenta
Mercury (Hg)Red
Arsenic (As)Yellow
Cadmium (Cd)Purple

The " why " has to do with the increased activities of small-scale illegal gold mining, also known as “galamsey”. This has heavily contaminated major Ghanaian river systems such as the Pra, Ankobra, and Birim river systems. These river systems supply drinking water, irrigation, and fish for millions of people in rural communities. The biosensor would serve as a cheap tool for screening tool for these communities.

Question 2. What living system would you use?

Answer

I would use a cell-free transcription-translation (TX-TL) system derived from an E.coli lysate. E. coli will be cultured, lysed, and clarified to produce a crude extract containing the ribosomal and metabolic machinery for transcription and translation. An energy mix of NTPs (nucleotide triphosphates), amino acids, cofactors, and plasmid DNA encoding the four metal-sensing circuits. Each circuit consists of two cassettes: Cassette 1, the reporter driven by the metal-responsive promoter.

Question 3. How would you use automation?

Answer

I would use an Opentrons OT-2 Liquid-handling robot to automate the reaction assembly and strip production process. This is because each biosensor strip requires precise, reproducible dispensing of microliter volumes of cell lysate and DNA reagent mix onto the paper substrate. The Opentrons OT-2 will ensure batch consistency and quality control, as it can run standardized dispensing programs across 96-well adjacent paper arrays with a plate reader to screen each batch for correct colorimetric responses across known metal standards before they are approved for lyophilization and distribution.

Question 4. How much would you need to make, and how long would it take?

Answer

For a first meaningful demonstration in a rural community near one of the polluted rivers, I would choose a target of 10,000 biosensor strips. This amount would be large enough to move beyond laboratory prototypes but small enough to represent a community-level pilot.

Each strip would have four sensing zones,

10,000 strips × 4 zones per strip = 40,000 sensing reatcion

If each sensing zone requires about 20 µL of cell-free reaction mixture

40,000 × 20 µL = 800,000 µL = 800 mL = 0.8 L

That would be 0.8 L of final cell-free reaction mixture required to manufacture 10,000 strips.

However, to account for any loss during the manufacturing process, I will add a 20% allowance for loss.

0.8 L × 1.2 = 0.96 L

Therefore, appoximately 1L of the formulated cell-free reaction would be needed.

For the duration, I would assume a complete cell-free sensing reaction would require 4 hours of incubation.

My initial manufacturing calculations would be: 4 hours biological reaction time 1 hour for automated setup and dispensing 12 hours of overnight freeze-drying 1 hour for assembly and packaging

Thus:

1 + 4 + 12 + 1 = 18 hours

It would take approximately 18 hours from reaction preparation to the packaging of a biosensor strip.

Question 5. What don’t you know yet?

I think some major unknowns I would need to investigate are

  • Shelf stability of the lyophilized reactions in the heat and humidity of Ghana’s rural zones.
  • How much variation, if any, occurs between the detection ability of each strip.

References