Week 1 assigment Valeria Quesada Ortega - Sj, Costa Rica.
Project. Development of a bioengineered gastronomic powder designed to create a multisensory dining experience without modifying the original ingredients.
the powder will consist of edible microcapsules made from food grade biopolymers that will remain stable during plating but dissolve when exposed to the normal pH of human saliva. Upon dissolution, the microcapsules will release microbursts with encapsulated umami compounds, such as glutamate extracts from algae or fermented foods.
Homework Questions from Professor Jacobson: 1.Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?
-DNA polymerase has an error rate of aprox one mistake per 108 nucleotides during DNA replication. This significant on the human genome which has around 3 x109 base pairs, so without correction, this woul result in a lot of mutations per replication. Biology addresses this discrepancy through multiple error correction mechanisms, such as post replication mismatch repair, to reduce the error rate to aprox one error per 10^9 nucleotides, maintaining th genomic stability.
Benchling and Silico Gel Art ##DNA desing challenge I chose mCherry because it is a red fluorescent protein derived from Discosoma sp. (a sea anemone). It is widely used in research as a fluorescent marker to visualize cells, proteins, and biological processes in real time under microscopy. It is stable, bright, and non-toxic to cells, making it ideal for cell biology experiments.
Subsections of Homework
Week 1 HW: Principles and Practices
Week 1 assigment
Valeria Quesada Ortega - Sj, Costa Rica.
Project.
Development of a bioengineered gastronomic powder designed to create a multisensory dining experience without modifying the original ingredients.
the powder will consist of edible microcapsules made from food grade biopolymers that will remain stable during plating but dissolve when exposed to the normal pH of human saliva. Upon dissolution, the microcapsules will release microbursts with encapsulated umami compounds, such as glutamate extracts from algae or fermented foods.
The goal of this gastronomic tech is not to correct poor cooking or override a chef’s creativity, but rather provide a precise finishing tool that amplifies the final sensory moment of a dish.
Governance
Primary governance goal
To ensure the bioengineered gastronomic experiences are safe, transparent and ethically deployed, while supporting creative culinary use.
Sub-goals
Prevent physiological harm to consumers
Ensure that the bioactive components do not accumulate or cause unwanted biological effects after consumption.
Promote informed consumer
Guarantee that consumers are aware they are consuming a bioengineered, interactive food component.
Avoid unnecessary barriers to culinary innovation
Ensure that governance measures do not disproportionately restrict chiefs and new culinary researchers.
Governance actions
Mandatory post consumptions biochemical deactivation.
Purpose
Currently, there is no standard requirement ensuring that bioactive food
components deactivate after ingestion. This actions proposes requiring
that the powder’s microcapsules re;iably deactivate once exposed to
salivary pH.
Design
We must incorporate a validated biochemical off switch (pH sensitive
biopolymer dissolution). Regulatory agencies would require
evidence of deactivations as part of food safety approval.
Assumptions
This assumes that salivary pH is likely consistent across individuals an
that deactivation mechanisms function reliably in diverse conditions.
Risks of failure and “success”
Failure would result in prolonged bioactivity or consumer harm, and even
successful implementation could limit certain experimental designs or
increase development costs.
Pre-market evaluation of sensory and metabolic safety.
Purpose
Gourmet food additives are not routinely assessed for individualized
biological interactions. This action proposes targeted safety testing
for bioengineered sensory .
Design
Independent labs would conduct standardized tests assessing metabolic
safety allergenicity, and sensory interaction. Approval would be required
prior to commercial use.
Assumptions
This assumes labs testing accurately represents experiences and population
diversity.
Risks of failure and “success”
Over-standarizations could reduce creative experimentation.
Transparent labeling and informed consent.
Purpose.
Consumers may not expect interactive bioeng components in their food.
This action ensures transparency.
Design.
Restaurants and us, as producers, would disclose the presence of
bioengineered sensory additives through menus or verbal explanation.
Assumptions
This assumes consumers understand the information and that disclosure
does not provoke unnecessary fear.
Risk of failure and “success”
Labeling could be ignored or misunderstood. Overemphasis could reduce
adoption despite safety.
Policy Goal
Action 1: Post-consumption deactivation
Action 2: Pre-market safety evaluation
Action 3: Transparency & consent
Enhance biosecurity
1
1
2
– Prevent incidents
1
1
2
– Enable response
2
2
2
Foster lab / production safety
1
1
2
– Prevent incidents
1
1
2
– Enable response
2
2
2
Protect human health
1
1
2
Minimize costs and burdens
3
3
1
Feasibility
2
2
1
Does not impede research or creativity
2
2
1
Promote constructive use
1
1
1
Conclusion.
Based on this evaluation, a combination of action 1 and action 2 should be prioritized, as they directly prevent harm and ensure consumer safety. Meanwhile, action 3 plays a complementary and important role by supporting transparency.
Week 1 Reflection.
During this first week, I thought a lot on the topics discussed, but particularly on the “dark side” of SynBiotech and Bioengineering. I also became more aware of how the limitation of these technologies significantly reduce progress, especially in Latin America, where structural and systemic barriers often restrict their reach.
Week 1 HW: Principles and Practices
Homework Questions from Professor Jacobson:
1.Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy?
-DNA polymerase has an error rate of aprox one mistake per 108 nucleotides during DNA replication. This significant on the human genome which has around 3 x109 base pairs, so without correction, this woul result in a lot of mutations per replication. Biology addresses this discrepancy through multiple error correction mechanisms, such as post replication mismatch repair, to reduce the error rate to aprox one error per 10^9 nucleotides, maintaining th genomic stability.
2.How many different ways are there to code (DNA nucleotide code) for an average human protein? In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
-Because the genetic code is degenerate, an average human protein of aprox 300 aminoacids can be encoded by a bunch of different DNA sequences creating a lot of different combinations, However, most of them do not function effectively. Factors such as codon bias, mRNA secondary strc, trasnlation spee, etc. limit which DNA sequences can successfully produce the desired protein. So, as a resultm only a small part of them are biologically viable.
Homework Questions from Dr. LeProust:
What’s the most commonly used method for oligo synthesis currently?
-The most commonly used method for oligonucleotide synthesis is solid-phase phosphoramidite chemistry
Why is it difficult to make oligos longer than 200nt via direct synthesis?
-Mainly due to error accumulation
Why can’t you make a 2000bp gene via direct oligo synthesis?
-Because the cumulative error rate would be extremely high
Homework Question from George Church:
What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
-histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and arginine
-Due to the fact that animal do not produce Lysine, the abscence of it can function as a killer switch for engineered organisms. as a form of contingency
Week 2 HW: DNA read, write and edit
Benchling and Silico Gel Art
##DNA desing challenge
I chose
mCherry
because it is a red fluorescent protein derived from Discosoma sp. (a sea anemone). It is widely used in research as a fluorescent marker to visualize cells, proteins, and biological processes in real time under microscopy. It is stable, bright, and non-toxic to cells, making it ideal for cell biology experiments.
Different organisms prefer different codons for the same amino acid. If mCherry’s original codons are rare in the host organism, ribosomes will produce the protein slowly or make errors. Codon optimization replaces rare codons with preferred ones for the chosen host, maximizing expression efficiency and protein yield.
I chose E. coli as the expression host because it is the most common, cost-effective, and well-characterized system for protein production in laboratory settings. Using Twist Bioscience’s Codon Optimization Tool while avoiding Type IIs enzyme recognition sites BsaI, BsmBI, and BbsI, the optimized sequence is:
