Week 1 HW: Principles and Practices

Part1: Assignment

1. The Project Concept:

Integrated Plant-Based Bone Scaffolds The field of regenerative medicine currently relies heavily on static bone scaffolds that provide structural support but lack the ability to interact with the biological environment. I propose the development of a 3D bioprinted smart scaffold designed from sustainable, plant-based materials. This system will serve a dual purpose by providing a physical matrix for bone growth and integrating biosensors for real-time physiological monitoring. By using materials like alginate or cellulose, this approach offers a personalized and environmentally responsible alternative to traditional synthetic implants.

Technical Phases:

• Phase 1: Structural Foundation. The scaffold is bioprinted using biodegradable plant polymers tailored to the specific geometry of a patient’s bone defect. This provides the necessary mechanical integrity to support new tissue formation.

• Phase 2: Biological Intelligence. Biosensors are embedded within the matrix to monitor variables such as pH levels, calcium concentration, and mechanical strain. Simultaneously, a controlled delivery system releases growth factors to promote rapid vascularization and bone density.

• Phase 3: Controlled Degradation. As natural bone tissue regenerates and takes over the load-bearing responsibilities, the scaffold undergoes programmed biodegradation. This leaves behind only healthy, natural bone without the need for secondary surgeries to remove permanent hardware.

2. Governance Goals for Ethical Bioengineering

To ensure this technology aligns with safety and ethical standards, the following governance goals have been established.

Goal A: Environmental Sustainability and Non-Toxicity

The project must ensure that the transition to plant-based materials does not result in unintended ecological or biological consequences.

• Sub-goal: Utilize biodegradable materials that break down into inert metabolites to avoid systemic toxicity.

• Sub-goal: Standardize sourcing methods to ensure that plant extraction does not disrupt local ecosystems or biodiversity.

Goal B: Clinical Efficacy and Patient Protection

The integration of active growth factors requires strict oversight to prevent adverse biological reactions.

• Sub-goal: Validate the biocompatibility of all plant-derived components to eliminate the risk of chronic inflammation or immune rejection.

• Sub-goal: Implement precise delivery protocols for growth factors to prevent unregulated cellular proliferation.

3. Proposed Governance Actions

Action 1: Regulatory Frameworks for Bio-Hybrid Materials

The primary purpose is to establish clear safety benchmarks for plant-based medical devices that do not fit into existing regulatory categories. This involves collaboration with the MHRA and FDA to define specific testing protocols for the degradation rates of cellulose-based implants. The design of this action requires rigorous longitudinal studies to confirm that the breakdown of these materials is safe over several years. One significant risk is that high regulatory hurdles may delay the delivery of these life-changing treatments to patients in need.

Action 2: Data Security Protocols for In-Vivo Biosensors

As these scaffolds generate continuous streams of patient health data, it is vital to establish ethical data handling practices. The design of this action includes the development of encrypted transmission standards to ensure that sensitive biological information is only accessible to authorized medical personnel. A key assumption is that patient data can be transmitted wirelessly without compromising the physical integrity of the scaffold. The risk of failure involves potential cybersecurity vulnerabilities that could expose private health metrics.

Action 3: Global Sustainability Certification

This action focuses on creating a “Green Biotech” certification to encourage the use of eco-friendly materials in the medical industry. By working with the United Nations Environment Programme, we can set international standards for the carbon footprint of medical manufacturing. This assumes that a global market exists for sustainable medical products. However, a potential risk is that the cost of obtaining such certifications could increase the final price of the scaffold, potentially limiting access for lower-income healthcare systems.

4. Scoring of Governance Actions

(Note: 1 represents the highest alignment with the goal)

5. Prioritization and Ethical Considerations

Upon reviewing the scores, Action 1 (Regulation of Biodegradable Biomaterials) is the highest priority. Without a validated safety profile and regulatory approval, the clinical and environmental benefits of the scaffold cannot be realized. While Action 3 is easier to implement, it remains secondary to the fundamental safety of the patient. During the development of this proposal, an important ethical concern arose regarding “Biotelemetry Equity.” If smart scaffolds become the gold standard, there is a risk that only patients in high-resource settings will benefit from real-time healing monitoring. To address this, governance actions should include incentives for companies to develop “passive” versions of the scaffold that provide high-quality structural support at a lower cost for global distribution. Relevant Audiences The recommendations for these governance actions are directed toward the FDA and the World Health Organization. These bodies are essential for establishing the international safety and sustainability standards required to bring 3D bioprinted plant-based scaffolds into mainstream clinical practice.

6. References

10.1109/SENSORS56945.2023.10325163

10.1002/adhm.202102807

https://cordis.europa.eu/project/id/101177877

Part2: Lab Preparation

It was not applicable for Committed Listeners

Part3: Week 2 Lecture Prep

Questions from Professor Jacobson

Q1: Even though it is not perfect, the precision of nature’s machinery for copying DNA is actually quite staggering. The intrinsic error rate of DNA polymerase is approximately one mistake for every million base pairs copied (10^(−6)). For context, the human genome comprises around 3.2 billion base pairs. If we were to depend solely on polymerase, each and every cell division would give rise to innumerable arbitrary mutations. This would have catastrophic consequences for the stability of life over many generations, but biology handles this massive discrepancy through a multi-layered proofreading and repair system. First, the polymerase itself has a ‘delete’ function whereby it can sense a mismatch, back up and correct it. Secondary systems, such as the MutS repair complex, then scan the DNA afterwards to detect any rare mistakes that have slipped through the first net. This combined effort brings the final error rate down to approximately one in a billion. This makes it reliable enough to maintain the blueprint of a human being.

Q2: When it comes to coding proteins, there is an incredible amount of flexibility because the genetic code is redundant. Since most amino acids are linked to several different three letter codons, you could theoretically write the DNA sequence for an average human protein in more ways than there are atoms in the universe. In practice, however, most of these sequences just do not work in a living cell. A major reason for this is the physical shape the RNA takes. If a sequence accidentally folds into a tight hairpin or a complex secondary structure, the cellular machinery gets physically stuck, much like a zipper hitting a snag in fabric. There are also issues with sequences having extreme GC ratios, which makes them too unstable or difficult for the cell to handle. Plus, cells have internal “cleavage rules” where they recognize certain patterns as signals to chop up the genetic instructions before they can even be translated. So, while the theoretical options are infinite, the actual biological grammar needed to express a protein is much more restrictive.

Questions from Dr. LeProust

Q1: The standard approach is the phosphoramidite method, which follows a four-step cycle. It starts with coupling the phosphoramidite to the chain, followed by capping any unreacted sites to prevent errors. The link is then oxidized to stabilize it, and finally, the growing chain is deblocked to prepare it for the next nucleotide addition.

Q2: The main issue is the cumulative effect of coupling efficiency. Even with a very high success rate for each step, small errors add up quickly over many cycles. By the time you reach 200 nucleotides, these compounding errors and the accumulation of truncated or incorrect sequences make it nearly impossible to retrieve a pure, full-length product.

Q3: Synthesizing a 2000bp gene directly would require 2000 consecutive coupling cycles without a single mistake, which is chemically unrealistic with current technology. The yield of the correct full-length molecule would be effectively zero. Beyond the chemistry, the sheer cost and the buildup of chemical damage over such a long process make it much more practical to assemble smaller fragments rather than trying to print the whole gene at once. The ten amino acids that are generally considered to be essential for animals are: arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. They are classified as essential because animals cannot synthesise sufficient quantities of their carbon skeletons, meaning they must be obtained through diet or from symbiotic relationships with microbes.

Questions from George Church

The ’lysine contingency’ refers to the fact that animals have lost the ability to produce lysine independently. From an evolutionary perspective, this seems less like a biological flaw and more like a way for ecosystems to create a reliance between different species. Our specific need for this amino acid has shaped the world as we know it, creating massive agricultural systems and complex food webs that would not exist if we could produce lysine ourselves. For example, the industrial production of lysine for livestock feed is a significant global enterprise centred on optimising animal growth. Without this essential amino acid, the entire economic and agricultural infrastructure might not exist, and we might not have moved towards such extensive farming practices. I wonder if, over millions of years, animals became dependent on lysine as a kind of self-imposed evolutionary trade-off. Perhaps it was once non-essential, but because it was so abundant in the environment, our ancestors eventually ’turned off’ the expensive metabolic machinery needed to produce it. In that sense, what we call a contingency is really just nature’s efficient way of outsourcing production to the surrounding environment.

References;

https://www.ncbi.nlm.nih.gov/books/NBK557845/

https://www.ncbi.nlm.nih.gov/books/NBK234922/