First, describe a biological engineering application or tool you want to develop and why After the first week of the How To Grow Almost Anything course and the projects that were presented by the panel, I decided to focus on an area that has always fascinated me: skincare and cosmetics. I have personally struggled to find products that actually worked for my skin. Some creams caused dryness, others triggered breakouts, and many were ineffective despite high prices and flashy marketing. Over time, I realized that this frustration is common—most skincare follows a “one-size-fits-all” approach, categorizing skin as oily, dry, combination, or sensitive. While these categories are a helpful starting point, they fail to capture the biological complexity and uniqueness of each person’s skin.
PART 1: Gel Art For the Gel Art part, I searched Roman’s Gallery and chose the little smiley face :).
PART 3: DNA Design Challenge 3.1 Choose Your Protein The protein I have chosen for this DNA design challenge is Sonic Hedgehog (Shh), a critical signaling molecule involved in embryonic development, tissue patterning, and organ formation. Shh plays a central role in directing cell fate decisions during development, and mutations in this protein are linked to severe developmental disorders. Its importance in biology, combined with the fact that it is well-characterized and has a known amino acid sequence, makes it an ideal candidate for this exercise.
Python Script for Opentrons Artwork I used the opentrons-art.rcdonovan.com site yo make a shrimp design: The script made with collab: from opentrons import types
Subsections of Homework
Week 1 Homework: Microbiome-Tuned Skincare week
1. First, describe a biological engineering application or tool you want to develop and why
After the first week of the How To Grow Almost Anything course and the projects that were presented by the panel, I decided to focus on an area that has always fascinated me: skincare and cosmetics. I have personally struggled to find products that actually worked for my skin. Some creams caused dryness, others triggered breakouts, and many were ineffective despite high prices and flashy marketing. Over time, I realized that this frustration is common—most skincare follows a “one-size-fits-all” approach, categorizing skin as oily, dry, combination, or sensitive. While these categories are a helpful starting point, they fail to capture the biological complexity and uniqueness of each person’s skin.
This personal challenge led me to explore a potential solution: microbiome-tuned skincare. This approach involves designing cosmetic formulations that are personalized based on an individual’s skin microbial ecosystem. Every person’s skin hosts a complex community of microbes, including bacteria, fungi, and viruses, which together influence hydration, barrier function, inflammation, and susceptibility to conditions like acne, eczema, or premature aging. Normal skincare does not account for this complexity and treats all skin as if it reacts the same way. Microbiome-tuned skincare, by contrast, supports beneficial microbes while balancing or reducing harmful ones.
For example, some individuals naturally have low levels of certain beneficial bacteria, such as specific strains of Cutibacterium acnes, which help maintain the skin barrier and prevent infection. Prebiotic creams may promote the growth of beneficial microbes. On the other hand, individuals with higher levels of pro-inflammatory microbes could use formulas containing anti-inflammatory compounds that rebalance the microbial ecosystem without harming beneficial organisms. By analyzing a person’s skin microbiome, products can be customized for their unique needs rather than relying on generic formulations.
From a bioengineering perspective, this project combines synthetic biology, computational biology, and personalized healthcare. Skin samples can be collected to identify microbial composition, and machine learning algorithms can predict how different formulations will interact with these microbial communities. The result is a personalized skincare routine that improves hydration, reduces inflammation, supports anti-aging processes like collagen maintenance, and maintains overall skin health. This approach transforms skincare from a trial-and-error routine into a scientifically guided, individualized experience.
Beyond cosmetics, microbiome-tuned approaches have broader applications. Dermatologists could use similar strategies to treat skin conditions such as eczema, rosacea, or chronic acne with higher precision. Another example is wound care: microbiome-tuned wound treatments use microbial profiling and predictive analytics to personalize care, supporting beneficial microbes while inhibiting harmful ones. Monitoring the wound’s microbial environment over time can prevent infection, accelerate healing, and reduce reliance on antibiotics. Personally, the appeal of this project is both scientific and social: it addresses a real-life problem that I have experienced and has the potential to help others avoid ineffective treatments.
The skin is the largest organ of the human body and serves as a defensive barrier against pathogens while supporting sensory functions. Its microbiome is essential for health because it:
Competes with harmful microbes, preventing infections
Communicates with the immune system, regulating inflammation
Supports barrier integrity, reducing dryness and irritation
Disruption of this microbial balance, known as dysbiosis, increases the likelihood of skin issues such as acne or eczema. Dysbiosis can result from diet, environmental factors, skincare products, or antibiotics. Regular skincare often addresses only symptoms rather than the underlying microbial imbalance. Microbiome-tuned skincare aims to restore balance and promote long-term skin health.
This strategy can be implemented using three main approaches:
Microbiome Sequencing: Collect skin samples and analyze microbial DNA to assess bacterial, fungal, and viral composition.
Machine Learning Analysis: Use computational models to predict how specific ingredients will affect microbial balance and skin health.
Personalized Formulation: Develop creams, serums, or cleansers specifically designed to support beneficial microbes and reduce harmful ones.
By focusing on maintaining the health of the skin ecosystem, microbiome-tuned skincare shifts the approach from reactive to proactive care.
2. Governance/Policy Goals
Because microbiome-tuned skincare directly interacts with the body, ethical considerations are critical. The main governance goals for this project are:
Preserving Consumer Health and Safety Skincare products based on microbiomes act as biological components. Poorly designed formulas may disrupt microbial balance, leading to irritation and other skin conditions. The skin microbiome is influenced by age, genetics, ethnicity or and environmental factors, so products must be tested widely and safely. Sub-goals include:
Standardizing validation procedures for personalized formulas
Monitoring long-term effects on skin health and microbial balance
Testing across diverse populations to ensure safety and effectiveness
** Privacy and Data Security** Microbiome data is personal and could reveal information about health, lifestyle etc. Protecting this information is essential. Sub-goals include:
Anonymizing microbial data
Implementing strict consent procedures for users
Preventing misuse by third parties or commercial entities
3. Governance Actions
Action 1: Regulatory Framework for Microbiome-Based Products
Purpose: Existing cosmetic regulations are not designed for personalized microbial interventions. A framework would define safety standards, acceptable microbial strains, and validation protocols.
Design: Regulatory agencies (FDA, EMA) would require companies to submit microbial and clinical data for approval. Long-term monitoring ensures continued product efficacy.
Assumptions: Regulators accept microbiome-based evidence; companies can standardize testing across populations.
Risks of Failure & Success: Overly strict regulations could slow innovation or increase costs, while overly permissive rules may allow unsafe products to reach consumers.
Action 2: Privacy and Data Protection
Purpose: Protect sensitive microbiome data and prevent misuse.
Design: Use encryption, anonymization, secure storage, and strict consent. Independent audits and international standards would guide compliance.
Risks of Failure & Success: Data breaches or misuse could harm consumers through discrimination. Strong protections build trust and encourage adoption of microbiome-based products.
Action 3: Incentives for Broad Access and Ethical Design
Purpose: Ensure microbiome-tuned skincare benefits a wide population, not only wealthy consumers.
Design: Provide grants, subsidies, and open-source tools for small companies or academic labs.
Assumptions: Financial and technical support will broaden equitable access.
Risks of Failure & Success: Limited funding or intellectual property disputes could restrict access. Successful implementation ensures broad social impact.
4. Governance Scoring
Policy Criteria
Option 1
Option 2
Option 3
Enhance Biosecurity
Preventing incidents
1
2
3
Helping respond to incidents
1
2
3
Foster Lab Safety
Preventing incidents
1
2
3
Helping respond to incidents
2
1
3
Protect the Environment
Preventing incidents
2
3
1
Helping respond to incidents
2
3
1
Other Considerations
Minimizing costs & burden to stakeholders
3
2
1
Feasibility
2
1
2
Does not impede research
1
2
1
Promotes constructive applications
1
2
1
5. Prioritization and Recommendations
Based on the scoring, I would choose a combination of Action 1 (Regulatory Framework) and Action 2 (Privacy and Data Protection), while keeping Action 3 (Equitable Access) as a secondary focus. Regulatory oversight ensures products are safe and effective, so it is preventing disruptions to the skin microbiome. Equity initiatives are important but should follow safety and privacy considerations to ensure broad access.
Trade-offs include higher costs and slower innovation, but these are necessary to avoid harm and ensure ethical deployment. Target audiences include federal regulators (FDA, EMA), companies for privacy compliance, research institutions for open-access tools, and international bodies for cross-border standards. This combination balances safety, privacy, innovation, and societal impact, making microbiome-tuned skincare both effective and responsible.
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, and how does biology deal with that discrepancy?
Polymerase has an error rate of roughly 1 in 10⁶ bases. The human genome contains roughly 3 billion base pairs, meaning about 3,000 mistakes could occur per replication. Biology corrects these errors with proofreading, apoptosis of damaged cells, and by allowing some variation to contribute to evolution.
2. How many different ways are there to code DNA for an average human protein? Why do all these sequences not work in practice?
Theoretically, about 10¹⁵⁷ DNA sequences could encode a 330-amino-acid protein. In practice, many sequences fail due to mRNA folding, premature translation stops, and codon bias that affects efficiency.
Dr. LeProust
1. Most commonly used method for oligo synthesis
The solid-phase phosphoramidite chemical synthesis is the most used technology today for making custom DNA oligonucleotides.
2. Why is it difficult to make oligos longer than 200 nucleotides?
In addition to side reactions and chemical limitations, it is challenging due to cumulative stepwise errors and yield drops. The maximum efficiency of each addition cycle in the synthesis of phosphoramidite is approximately 99%. The likelihood of creating an accurate product decreases to a maximum of 14% over 200 bases. The increasing length of the chain in conventional porous supports can also obstruct reagent access, which reduces efficiency even more.
3. Why can’t you make a 2000 bp gene via direct oligo synthesis?
Based on the previous answer, accumulating errors make a 2000 base pair gene (4000 nucleotides) almost impossible to synthesize. It is simply not feasible.
George Church
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 10 essential amino acids that animals cannot synthesize and must obtain through their diet are arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. The “Lysine Contingency” in Jurassic Park involved engineering dinosaurs to be unable to produce lysine so that, without lab-supplied supplements, they would die if they escaped. While this is a clever narrative device, it is biologically flawed because lysine is abundant in natural foods, meaning escaped dinosaurs could easily obtain it and survive. This highlights that while lysine is essential for all animals, relying on its absence as a control measure overlooks basic nutritional biology and ecosystem realities. A more effective contingency would need to target something unique to the lab environment rather than a common dietary requirement.
Week 2 Homework: DNA Read, Write & Edit
PART 1: Gel Art
For the Gel Art part, I searched Roman’s Gallery and chose the little smiley face :).
PART 3: DNA Design Challenge
3.1 Choose Your Protein
The protein I have chosen for this DNA design challenge is Sonic Hedgehog (Shh), a critical signaling molecule involved in embryonic development, tissue patterning, and organ formation. Shh plays a central role in directing cell fate decisions during development, and mutations in this protein are linked to severe developmental disorders. Its importance in biology, combined with the fact that it is well-characterized and has a known amino acid sequence, makes it an ideal candidate for this exercise.
Using the amino acid sequence from UniProt, I performed a reverse translation to determine the nucleotide sequence that could encode Shh. Reverse translation is the process of inferring a DNA sequence from a protein sequence, based on the codons that encode each amino acid. Because multiple codons can code for the same amino acid, this step may produce several possible DNA sequences. The resulting DNA sequence represents the gene that could be transcribed and translated to produce the Shh protein, reflecting the principles of the Central Dogma, where DNA is transcribed into RNA and RNA is translated into protein.
Once the DNA sequence is determined, I codon-optimized it for E. coli expression. Codon optimization is important because different organisms prefer certain codons over others for the same amino acid. Using preferred codons in E. coli increases translation efficiency, improves protein yield, and avoids rare codons that can slow ribosomes or create secondary structures. This ensures robust expression of Shh in bacterial systems.
3.4 You Have a Sequence! Now What?
With a codon-optimized Shh sequence, several methods can be used to produce the protein:
Cell-dependent expression: Clone the DNA into a plasmid vector and introduce it into E. coli. The bacterial machinery transcribes the DNA into mRNA and translates it into Shh protein.
Cell-free systems: Produce Shh protein directly in vitro using transcription-translation mixtures from E. coli lysates.
Both approaches demonstrate how a nucleotide sequence can be converted into a functional protein through natural molecular processes.
3.5 How Does it Work in Nature
In nature, the Shh gene is transcribed into mRNA and translated into a precursor protein, which then undergoes post-translational modifications, including cleavage and lipidation. These modifications are required for proper secretion and signaling activity. This illustrates how a single gene can produce a biologically active protein, highlighting the flow of information from DNA → RNA → protein and the importance of transcriptional and post-translational regulation.
PART 4: Prepare a Twist Synthesis Order
PART 5: DNA Read, Write, and Edit – Microbiome Skincare Applications
5.1 DNA Read – Sequencing
DNA to sequence and why: I would sequence skin microbiome DNA from individuals with different skin types or conditions, such as acne-prone, sensitive, or aged skin. This allows identification of beneficial and harmful microbes, their functional genes, and metabolites affecting skin health. Sequencing this DNA can inform development of probiotic treatments, personalized skincare, and microbial-derived bioactives.
Sequencing technology and details: I would use Oxford Nanopore long-read sequencing, a third-generation method that can read full-length microbial genomes and plasmids. Input DNA would be extracted from skin swabs, lightly sheared, and ligated with nanopore adapters. Essential steps include passing DNA through a protein nanopore, measuring ionic current changes, and decoding bases from these signal variations. The output is long-read sequences of microbial genomes and plasmids, helping resolve strain-level diversity. Limitations include lower per-read accuracy compared with short-read sequencing, but high coverage and error-correction mitigate this.
5.2 DNA Write – Synthesis
DNA to synthesize and why: I would synthesize genes encoding skin-beneficial metabolites, such as bacterial enzymes producing natural moisturizers, antioxidants, or antimicrobial peptides. For example, a sequence coding for a bacterial ceramide-synthesizing enzyme could be used to engineer probiotic strains that restore skin barrier function. This approach could create living or topical treatments that enhance skin health naturally.
Technology for synthesis and details: I would use Twist Bioscience’s array-based high-throughput DNA synthesis. Essential steps include sequential nucleotide addition via phosphoramidite chemistry, oligo cleavage and purification, and assembly into full-length gene constructs. Limitations include sequence length constraints (<200 bases per oligo), potential synthesis errors, and optimization requirements when expressing microbial genes in target probiotic strains.
5.3 DNA Edit – Editing
DNA to edit and why: I would edit the genome of commensal skin bacteria like Staphylococcus epidermidis to enhance production of anti-inflammatory molecules or UV-protective compounds. This could reduce acne, eczema flare-ups, or sun-induced skin damage while maintaining microbiome balance. Edits might include upregulating genes for antimicrobial peptides or protective pigments.
Technology for editing and details: I would use CRISPR-Cas9 coupled with plasmid-based delivery, a precise genome editing tool for bacteria. Essential steps include designing guide RNAs targeting regulatory regions, delivering Cas9 and repair templates into bacterial cells, and screening for successful edits. Inputs include plasmids carrying Cas9, guide RNAs, and donor DNA. Limitations include variable editing efficiency across bacterial strains, potential off-target mutations, and challenges in ensuring stable long-term expression of engineered traits.
Week 3 Homework: Lab Automation
Python Script for Opentrons Artwork
I used the opentrons-art.rcdonovan.com site yo make a shrimp design:
##############################################################################
### PATTERNING
##############################################################################
drop_volume = 4
for color, coordinates in design_data.items():
# Pick up a new tip for each color
pipette_20ul.pick_up_tip()
source_well = location_of_color(color)
for (x, y) in coordinates:
pipette_20ul.aspirate(drop_volume, source_well)
dispense_location = center_location.move(
types.Point(x=x, y=y, z=0)
)
dispense_and_detach(
pipette_20ul,
drop_volume,
dispense_location
)
# Drop tip before switching colors
pipette_20ul.drop_tip()
Post-Lab Questions
1.Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.
For this part I chose the paper: Shotgun Proteomics Sample Processing Automated by an Open‑Source Lab Robot, Han et al., Journal of Visualized Experiments, 2021. The study focuses on automating shotgun proteomics workflows using the open-source Opentrons OT‑2 liquid handling robot. Shotgun proteomics is a widely used technique for identifying and quantifying large numbers of proteins in complex samples such as tissues or cell lysates. Traditional workflows are labor-intensive, including protein extraction, concentration measurement, chemical reduction and alkylation, enzymatic digestion, and peptide clean-up. Manual handling introduces variability and errors, which can affect reproducibility and data quality. Han et al. addressed these issues by developing a semi-automated workflow on the OT‑2, reducing manual labor, improving consistency, and making proteomics automation more accessible for academic labs.
The OT‑2 robot provides a platform for automated liquid handling. Han et al. configured the OT‑2 with single-channel electronic pipettes, a magnetic module, a temperature module, and specialized tube racks and deep-well plates. Their automated workflow included three main steps:
Protein reduction, alkylation, and digestion: proteins were prepared for enzymatic cleavage into peptides. Peptide clean-up using SP3 paramagnetic beads: proteins in common detergents can interfere with downstream analysis. LC-MS/MS analysis: After automation, peptides were dried, reconstituted, and analyzed by LC-MS/MS
Three Python scripts supported the automation: NoSP3_digestion.py, SP3_peptide_cleanup.py, SP3_digestion.py .
Han et al., 2021, demonstrate that low-cost open-source robots like the OT‑2 can automate complex proteomics workflows effectively. Their study highlights the benefits of automation: consistent sample preparation, reduced manual labor, flexibility for different sample types, and affordable access for academic or resource-limited laboratories.
2.Write a description about what you intend to do with automation tools for your final project. You may include example pseudocode, Python scripts, 3D printed holders, a plan for how to use Ginkgo Nebula, and more. You may reference this week’s recitation slide deck for lab automation details.
Final Project Ideas
Idea I: A Programmable Probiotic Platform for Microbiome-Modulated Skincare
My first idea is a project that explores how engineered living systems can be used to modulate the skin microbiome. Instead of relying on chemical antimicrobials, this project proposes a programmable probiotic designed to selectively respond to acne-associated microenvironments. Acne is often linked to dysbiosis and inflammatory strains of Cutibacterium acnes, rather than the mere presence of bacteria. The system uses a skin-safe bacterial chassis engineered with a pH-sensitive genetic circuit. When exposed to the slightly acidic conditions characteristic of inflamed acne lesions, the circuit activates expression of a targeted antimicrobial peptide.
My second idea is a synthetic biology project that creates living flowers that glow in response to environmental triggers, such as allergens, pollutants, or changes in pH. Instead of passive decoration, these flowers act as living biosensors, showing you what’s happening around them. The flower’s cells are engineered with a genetic circuit that detects a specific trigger, like pollen proteins or chemical pollutants. When the trigger is present, the circuit switches on and activates bioluminescent genes, making the flower glow. The glow stops when the trigger is gone.
My third idea is a living, edible fungal patch designed to produce essential vitamins such as B12, B9 and K2. Fungi are grown in small hydrogel scaffolds containing optimized nutrients, which support both growth and vitamin synthesis. As the patch develops over several days,it can be observed the living system in action, with growth and optional color indicators reflecting vitamin production.
