I am a multidisciplinary designer who developed an interest in circular design, biodesign, systems thinking and speculative design and the parallels these studies have.. My current work is focussed on speculating the use of Biodesign in the immediate future in terms of material design.
Week 1 HW: Principles and Practices
1.Biological engineering tool/application I am trying to develop a dyeing method for fabrics and surfaces by using Physarum Polycephalum, or the slime mould as an activator. The aim is to let the slime mould create one-of-one designs by growing on the surface, letting a level of unpredictabiity of growth control the outcome. Slime moulds are very good at creating pathways while expanding in search of optimum survival conditons. During this travel, they tend to leave behind residual pigment, usually yellow in colour. After drying it looks something like this. In this bioengineered application, physarum polycephalum expresses a pigment forming enzyme(tyrosinase/laccase-type oxidase) that catalyzes the oxidation of benign phenolic or cathechol precursors into reactive quinones that polymerize into and insoluble melanin-like pigment.
Week 2 HW: DNA read-write-edit
Part 1: Gel Electrophoresis Due to no access to equipment and space for gel electrophoresis I simulated the same to understand the process on https://www.labxchange.org/library/items/lb:LabXchange:9548bee3:lx_simulation:1?fullscreen=true Workflow Design plasmid DNA with protein of interest →Transform bacteria with plasmid DNA→Get many copies of plasmid DNA→introduction of plasmid DNA to cells
I am trying to develop a dyeing method for fabrics and surfaces by using Physarum Polycephalum, or the slime mould as an activator. The aim is to let the slime mould create one-of-one designs by growing on the surface, letting a level of unpredictabiity of growth control the outcome. Slime moulds are very good at creating pathways while expanding in search of optimum survival conditons. During this travel, they tend to leave behind residual pigment, usually yellow in colour. After drying it looks something like this.
In this bioengineered application, physarum polycephalum expresses a pigment forming enzyme(tyrosinase/laccase-type oxidase) that catalyzes the oxidation of benign phenolic or cathechol precursors into reactive quinones that polymerize into and insoluble melanin-like pigment.
The target surface/fabric is to be first coated with a reservoir layer (mild binder+humectant) that is stable and non-coloured when dry. As the plasmodium (active foraging stage of slime mould), it leaves back a hydrateed, anionic extracellular slime film (acidic polysaccharide rich) that locally rehydrates the layer and provides a high water, ionically active environment for the reaction to take place. Enzyme delivered at the surface via organism converts the reservoir layer into pigment only with the trail’s footprint, and the newly formed polymer precipitates in place. The slime’s polyanionic matrix and the binder layer together act as immobilizing scaffold, physically and electrostatically retainining the pigment on fibres so the organism still moves while the dyed path remains as a persistent spatial record of its presence.
2.Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy.
Ensuring rigourous quality tests ensuring the engineered organism/pigment polymer/enzyme does not create risks like allergens/irritation, sensitizers, or use unsafe binders/precursors with result in volatile+unpredicatble by-products. Developing narrow function envelope for the to curb new emergent pathways that may produce undocumented results. Create a timeline documenting the processes that have been enacted and by which actors. Ensure “program changes” cannot be done by end-users (e.g., no easy swapping of genetic payloads or addition of external DNA to redirect production).
Developing systems that prevent accidental spread/mishandling of the GMO from the process of R&D to Distribution to end-of -life. (Develop clear handling protocols, containment during demonstrations and training, maintaining workspaces etc.) Ensuring design features that reduce aerosolization/smearing (sealed edges, protective breathable membranes, simple decontamination steps for handlers). Making failure modes public will also ensure the same errors are not repeated
Ensuring all the agents used in the process especially the GMO go through assess,,emt of whether it can sporulate in local environments and accordingly come up with stronger safeguarding.
Assessing toxicity levels for precursors and binders to avoid accumulative compounds post end-of-life. Ensuring biological activity is terminated before disposal and the waste is integrated with local waste stream systems.
Option 1: Tiered containment + targeted efficacy Option 2:DNA Synthesis screening + Dual genetic safeguard requirement Option 3:Standardizing end-of-life management
1 = strongest , 3 = weakest
| Does the option: | Option 1 | Option 2 | Option 3 |
|---|---|---|---|
| Enhance Biosecurity | |||
| • By preventing incidents | 1 | 1 | 1 |
| • By helping respond | 2 | 1 | 1 |
| Foster Lab Safety | |||
| • By preventing incident | 1 | 1 | 3 |
| • By helping respond | 2 | 1 | 3 |
| Protect the environment | |||
| • By preventing incidents | 1 | 3 | 1 |
| • By helping respond | 1 | 3 | 1 |
| Other considerations | |||
| • Minimizing costs and burdens to stakeholders | 2 | 3 | 3 |
| • Feasibility? | 2 | 3 | 2 |
| • Not impede research | 2 | 3 | 2 |
| • Promote constructive applications | 1 | 1 | 1 |
A radial graph to show the level of involvement of different actors in enforcing policies
My choice of policies is to combine Dual safeguard and screening of developed application + Standardizing end-of-life management Choosing option 1 would reduce the scope of innovation, but Option 2 that ensures thourough assessment of the modified product whcih enables it to be replicated and scaled widely. It also mitigates concerns like pathogenic propogation risks, mutations in local environments, and/or any unintended consequences since a standardized model of development will be certified and followed.
DNA Polymerase has an inherent error rate of 1 in (10^{5}) to (10^{6}) bases. Human genome’s size is (\approx 3\times 10^{9}) base pairs. If replication is 100 percent efficient 0 errors would occur. With mistakes at (10^{-5}) rate it would result in 30,000 to 50,000 errors. Due to post replication mismatch error the final error rate in human cells is reduced to less than 10 mutations per genome per replication. To deal with this, enzymes ((\delta ) and (\epsilon )) check each nucleotide as they go, removing mispaired bases instantly, increasing accuracy 100-fold. After replication fork passes special repair proeins scan newly synthesized DNA for mismatches that slipped past the proofreading step and throughout the cell cycle other mechanisms like base excision repair nucleotide excision repair fixes spontaneous damage that could possibly cause a failure.
An average human protein (~450-500 amino acids) can be coded by different DNA sequences, potentially exceeding (10^{100}) possibilities, due to the genetic code’s degeneracy (61 codons for 20 amino acids). The reasons for failure to produce functional proteins are due to cases of improper protein folding, premature stop codons, incorrect splicing etc.
Due to no access to equipment and space for gel electrophoresis I simulated the same to understand the process on https://www.labxchange.org/library/items/lb:LabXchange:9548bee3:lx_simulation:1?fullscreen=true
Workflow
Design plasmid DNA with protein of interest →Transform bacteria with plasmid DNA→Get many copies of plasmid DNA→introduction of plasmid DNA to cells
After signing in I imported it into Benching and ran digests for EcoRI HindIII BamHI KpnI EcoRV SacI SalI
And then ran digests on SalI SacI BamHI KpnI EcoRV BamHI KpnI SacI SalI
to create an Elephant! 🐘
For this, I referred to an iGem video to understand how enzyme digesting works as well https://www.youtube.com/watch?v=7cGev-SKLao
Chosen protein : Actin
tr|D3BD07|D3BD07_HETP5 Actin OS=Heterostelium pallidum (strain ATCC 26659 / Pp 5 / PN500) OX=670386 GN=act10 PE=3 SV=1 MEGEDVQALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHTGVMVGMGQKDSYVGDEAQ SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVSHTVPIYEGYALPHAILRLD LAGRDLTDYMMKILTERGYSFTTTAEREIVRDIKEKLAYVALDFENEMQTAASSSALEKS YELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTYNSIMKCDVDIRKDLYGNVVL SGGTTMFPGIADRMQKELTALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK EEYDESGPSIVHRKCF
Reverse translated
ATGGAAGGCGACGTTCAAGCGCTGGTGATCGACAATGGTTCTGGCATGTAAAGCGGGTTTCGCAGGCGACGACGCACCGCGCGCGCGCGTTCTTTCCTTCGATTGTGCGCCGTCGCCGTCATACCGGCGTGATGGTTGTGGGGATGCAGCAAGAGGACTCCTACGTGGGCGACGAGGCGCAGTCGAAAGGTGGGATCCTGACCCTGAAGTACCCGATCGAACACGGGATTGGTGACTAACAATGGGACGATATGAAGGAAATCTGGCACCACACGTTCTTATAACGAATTAAGAGTGGCGCCGGAAGAACCAGTTCCTGTGCTGCTGACCGAGGCGCCGCTGAACCCGAAAGCCAACCGTGAAGAAATGAAGACCAGGATTATGTTTGAACCTTTC AACACGCCGGCGATGTATGTGGCGATTCAAGCGGTGTTGTCGCTGTATGCCTCGGGTCGTACCACC GGTATTGTGATGGATTCTGGCGACGGCGTGTCCCATACGGTGCCCATCTATGAAGGTTATGCCTTACCGCACCGCATCCTCCGCCTGGATCTGGCGGGTCGCGATCTGACTGAC TATATGATGAAGATCCTGACTGAACGTGGTTATTCGTTTACGACCACCGCCGAAAGGGAaatcgtcgacatc aaagagaagctggcgtatgtggcacttgatttcgagaacgagatgcaaacggcggcgTCGTCGTCGTCGCGTTGAA AAGTCG TATGAACTGCCG GACGGCCAGGTCATCACTATCGGTAACGAACGTTTC CGCTGCCCTGCGCTTTCAACCGTCGTTCTTAGGCATGGAAAGCGCGGGCA TACACGAAACCACGTACAACAGCATTATGAAATGC GATGTCGACATT CGCAAGGATCTGTATGGTAACGTGGTCCTGGGCGGCACCACGATGTTCCCGGGCATCGCCGAACG CATGCAAGAAACTGACCACCGCGCTGGCGCCGTCGACCATGAAAATCAAGATCATTGCCGCGCCGGAACGTAAGTCTTGGGTCATCGGCGGC TCGTTGGCCTCGTCGACCTTC CAGCAGATG TGGATCAGCAAAGAAGAG TATGACGAAAGCGGTCCTTCGGTGATCCACCGTAAGTTCTTCGCGAAACCGCAAGATTAA
optimized codon sequence
Optimized DNA Sequence (1122 bp)
atggaaggcgatgtccaggcgctggtgatcgacaacggctccggcatgaaggccggcttcgccggcgatgatgcccccagggcggcggtgtcttcccctcgatcgtgggccgtccgcgtcacaccggtgtgatggtggtgggtatgcagcagaaagattcctatgtgggcgacgaagcgcaatcgaaagggcatcctgaccctgaagtatccgatcgagcatggcatcgtgaacaactgggacatggagaagatctggcaccacatgttctacaacgagctgcgtgtggcgccggaagaaccccacgtgctgctgaccgaggcgccgctgaacccgaaggccaaccgtgaacgcaagatgaagaccaggatcatgatgttcgaacagttcaacacgccggcgatgtatgtggcgattcaagcggtgctgtcgctgtatgcctcgggccgtaccaccggcatcgtgatggactccggcgatggcgtttcccacatcgtgcccatctatgaaggctatgcgctgccgcatgccatcctgcgcctggatctggcgggcagggatctgaccgactacatgatgaagatcctgaccgaacgcggttatagcttcaccaccaccgcggagaagatcgtccgggacatcaagaagaaactggcgtatgtggcgctcgatttcgaaaacgaaatgcaagcgaccgcgagctcgagcgccctggagaagtcgtatgagctgccggacggccaggtgatcaccatcggcaacgaacgcttccgttgccctgccgctgttccagccctcgttcggcatggagagcgccggcatccatgagaccacctacaacagcatcatgaagacctgcgatgtggacatccgcaaggacctgtatggcaacgtggtgctcggcggcaccaccatgttccccggcatcgccgacaggatgcaaaaggagctgaccgccgcgctgccgcccagcaccatgaagatcaagatcatcgcgccgccggagcgtaagtcgtgggtgatcggcggctcgctggcgagcctgagcacgttccagcagatgtggatcagcaaggaggaatacgacgagtcgggcccgagcatcgtgcaccgcaagtgcttcggcaagcgcaagatgaa