Week 1: Principles and Practices

1. General Objective To develop a grape-pomace biocuir with antimicrobial properties through the incorporation of metabolites produced using synthetic biology techniques, intended for the fabrication of tablecloths, kitchen coverings, and bathmats to improve community health among the Kumiai Indigenous population in San Antonio Necua, Baja California, Mexico.

2. Objective of Introducing Antimicrobial Metabolites To incorporate antimicrobial metabolites into the grape-pomace biocuir developed by Xquenda_Lab at El Colef, in collaboration with the Autonomous University of Baja California (UABC) and the Kumiai community of San Antonio Necua.

3. Concept and expected outcome of the project (Copilot prompt: how to incorporate synthetic biology principles into the production of an antimicrobial biocuir based on grape pomace using the following biocuir recipes developed by Xqueda_lab)

The project develops a biocuir made from grape pomace, reinforced with natural biopolymers (gelatin, starch, glycerin, natural latex) and enriched with antimicrobial metabolites produced through synthetic biology principles in wet lab facilities at Autonomous University of Baja California (UABC). These metabolites—purified and microencapsulated—are incorporated into the orujo based bioleather to create protective surfaces that reduce bacterial and fungal proliferation in rural domestic environments.

The antimicrobial Metabolites developed and introduced into the biocuir will be: • For kitchen surfaces (gastrointestinal risks): o Lactic acid o Acetic acid o Mild terpenes (limonene, low dose carvacrol) • For bathroom and humid surfaces (respiratory and fungal risks): o Biosurfactants (surfactin or sophorolipids) o Antifungal terpenes (thymol, carvacrol)

These compounds will be produced using GRAS microorganisms genetically engineered in UABC wet laboratory. Only purified metabolites are transferred to Xquenda_lab and the Kumiai community to be incorporated into the biocuir -never living organisms. Expected Outcome.

A community oriented antimicrobial orujo based biocuir, produced by Kumiai indigenous people in Xquenda_Lab – El Colef facilities at the Gadalupe Valley, in coordination with researchers from UABC. The biocuir will be used as: • Antimicrobial tablecloths • Kitchen surface covers • Bathroom mats • Protective domestic surfaces The antimicrobial orujo based biocuir is: • Microbially protective • Biodegradable and safe • Adaptable and manufacturable by the Kumiai community in Xquenda_lab - El Colef facilities at the Gaudalupe Valley. • A vehicle for citizen science learning, community health improvement, and social entrepreneurship owned by the Kumiai community from San Antonio Necua and Xquenda_lab.

GOVERNANCE AND ETHICS PROPOSAL (Copilot prompt: how to devrlop a governance system including Xquenda_lab, El colef, the Kumiai community and UABC as stakeholders to make a safe and ethical production of the Antimicrobial Biocuir Based on Grape Pomace making use of Synthetic Biology techniques to produce Metabolites)

Synthetic Biology for Community Benefit in an Indigenous Context A. Guiding Principles • Kumiai autonomy and collective decision making • Precaution and non harm • Radical transparency • Technology transfer • Epistemic equity (Indigenous knowledge = scientific knowledge) • Community benefit and shared outcomes • Respect for cultural identity and territorial rights

B. Actors and Responsibilities

1. Kumiai Community of San Antonio Necua • Collective decision making • Defining needs, uses, and priorities • Cultural and practical evaluation of prototypes • Right to pause, modify, or redirect the project

2. Xquenda_Lab (Public and Citizen Laboratory) • Space for technology transfer • Training in biomaterials and basic synthetic biology principles • Community based production of biocuir • Accessible documentation

3. UABC (Biologists, Engineers, Biotechnologists) • Genetic design and metabolite production • Exclusive handling of genetically modified organisms • Purification and characterization of metabolites • Ensuring biosafety and regulatory compliance

4. Project Governance Council • Kumiai representatives • Xquenda_Lab researchers • UABC researchers • El Colef observer

Functions of the Governance council: • Approve project directions • Evaluate risks and benefits • Oversee technology transfer • Validate educational materials • Resolve ethical questions

7. Biosecurity and Scientific Ethics Committee • Review genetic constructs and metabolic pathways • Supervise handling of organisms in wet lab settings • Ensure safe disposal of biological waste • Continuous risk assessment

C. Key Governance Processes

1. Collective Informed Consent • Open assemblies • Clear explanation of synthetic biology and metabolites • Recorded community agreements

2. Technology Transfer • Hands on training in Xquenda_Lab • Accessible manuals • Formation of local “technology stewards”

3. Transparency and Communication • Open information on processes, risks, and results • Pedagogical materials in clear language

4. Intellectual Property and Data • Explicit recognition of Kumiai contributions • Avoid exclusionary patents • Explore communitarian, co ownership or open licenses • Protection of sensitive cultural knowledge

5. Community Benefits • Priority use in Kumiai comunities and households • Potential Kumiai/Xquenda product line • Fair distribution of income if commercialization occurs

Note: This is just a firt conceptual approach. I understand that might be very difficult to produce those metabolites. Therefore I might have to choose only one to produce it in large scale in order to encapsulated and include it into the biocuir.

Preparation for lecture 2:

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? There are difere types of polomerase qualities and all of them have some kind of error. The leng of human genome is about 3.2 nillion pairs. Therefore corrections has to be made in any edition. Synthetic Biology deals with this big discrepancy by making corrections. For example a 10ns Base addition to the 1:10 error rate in the case of correcting Polimerase error in Biology synthesis as is shown in the slide 8 of the presentation.
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? There are two main different ways when it comes to code DNC: Chip based and non-chip based. In the case of the former many types of erros may happen depending of the choosen method; e.g. correction, reduction.

Homework Questions from Dr. LeProust:

1. What’s the most commonly used method for oligo synthesis currently? Direct synthesis using wall plate. 96 wale plate makes 1 gen. With a silicon platform it is possible to have 1M oligos in a chip to make 9.600 genes.
2. Why is it difficult to make oligos longer than 200nt via direct synthesis? Because chemical DNA synthesis is not perfectly efficient, and small errors accumulate with every added nucleotide. After ~200 cycles, the product becomes too impure and too heterogeneous to be useful (Direct answer from Copilot)
3. Why can’t you make a 2000bp gene via direct oligo synthesis? Because chemical synthesis cannot reliably produce a single, accurate 2000 base molecule. The error rate and truncation rate make it chemically impossible (Direct answer from Copilot)

Homework Question from George Church: Choose ONE of the following three questions to answer; and please cite AI prompts or paper citations used, if any.

1. [Using Google & Prof. Church’s slide #4] What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?

The “PVT TIM HALL” (Direct answer from Gemini to the question What are the 10 essential amino acids in all animals) The “PVT” Group • P – Phenylalanine: This is a precursor for signaling molecules like dopamine and adrenaline; it’s basically a building block for the “brain chemicals” that keep an animal alert. • V – Valine: One of the three “branched-chain” amino acids (BCAAs). It focuses on muscle growth, tissue repair, and providing extra energy when the body is stressed. • T – Threonine: This is a major component of structural proteins like collagen and elastin. It’s also vital for maintaining a healthy gut lining.

The “TIM” Group • T – Tryptophan: Best known as the precursor to serotonin. It helps regulate mood, sleep, and even the “fullness” feeling after eating. • I – Isoleucine: This BCAA is heavily concentrated in muscle tissue and is essential for producing hemoglobin (the stuff in blood that carries oxygen). • M – Methionine: A sulfur-rich amino acid that is crucial for metabolism, detoxifying the liver, and helping the body absorb minerals like zinc.

The “HALL” Group • H – Histidine: This is used to produce histamine, which is vital for the immune response, digestion, and maintaining the protective “sheaths” around nerve cells. • A – Arginine: While adult humans can make some, most animals (and human infants) need it from food to help remove toxic ammonia from the body via the urea cycle. • L – Leucine: Often called the “spark plug” for protein synthesis, this is the main amino acid that tells the body to start building and repairing muscle. • L – Lysine: This one is critical for bone health, the production of antibodies to fight off sickness, and the overall creation of enzymes and hormones. I believe the Lysine contingency hypothesis is very interesting if we think about it in relation to the Anthropocene and all the radical changes that are occurring in the world due to human activity. To think about the future where sources provide one of those 10 essential amino acids triggers some questions about how to synthetize and produce in a very efficient way some alternative source to get those amino acids. It also triggers some questions about the possibilities for humans to inhabit other planets and the importance of being sure about how to create an artificial environment able to produce in an efficient and sustainable way sources for those 10 essential amino acids.

3. [Given slides #2 & 4 (AA:NA and NA:NA codes)] What code would you suggest for AA:AA interactions?