Week 1 HW: Principles and Practices

Phage Therapy

1. Biological engineering application or tool.

Phage therapy has emerged as one of the most promising precission medicine with applications in health and agriculture. I believe phage therapy is going to be the state of the art technology in the future to solve disieases. Im particularly interested in the design of delivery sistems for phages. I have worked with biodegradable polymers such as alginate and chitosan. However I want to explore other systems such as lipidic nanoparticles and stabilization in different natural extracts or essential oils. I am currently working in this field, and I am really passionate about how material sciencies and nanotechnology can help improving efficiency of phages. I have worked with a variety of characterization techniques such as UV-Vis, FTIR, XRD, TGA, Potenciostat, SEM, TEM and sinthesis techniques such as Electrospinning. I truly believe that improving the system in wich is the phage, can help the phage itself. I also have a multidisciplinar focus, not only considering the laboratory, but also modeling and simulating the delivery sistem in silico.

2. Governance / Policy Goals

The governance goals are focused on ensuring that phage therapy applications are safe, effective, and ethically responsible.

• Improve Biosafety: Establish a multidisciplinary ethics committee (including experts in biotechnology, biosafety, ethics, and law) to evaluate and ensure that phage therapy is not misused or used dangerously. This committee should also periodically review the use of the therapy, adapting to new advances and ensuring that unforeseen risks do not arise.

• Promote Laboratory Safety: Ensure that laboratories working with phage therapies implement safe practices, aligned with international Good Laboratory Practice (GLP) guidelines. Implementing regular audits to verify compliance with these practices is crucial to ensuring ongoing safety.

• Protecting the Environment: Ensure that no toxic byproducts are generated during the isolation, purification, analysis, encapsulation, stabilization, and final delivery of the therapy. Furthermore, ensure that all biological waste is disposed of properly, following international standards and current environmental regulations. It would also be useful to assess the ecological footprint of the entire process to adjust practices according to new scientific findings.

• Fair Trade: Integrate phage-based products for biocontrol and protection of organic crops, ensuring they comply with Fair Trade regulations. This would not only contribute to sustainability but also improve the conditions of producers through ethical and accessible trade.

• Supply Chain: Utilize blockchain technology to guarantee transparency in processes, from therapy development to commercialization. This system will not only help ensure traceability but will also strengthen consumer trust and prevent fraudulent practices, while fostering a more ethical production ecosystem.

• Other Considerations: Minimize costs and burdens for the parties involved, ensuring the project’s economic viability.

3. Actors + Actions

Actor 1. Farmers

• Action 1: Adopt responsible application practices for phage therapy biocontrol

  • Purpose: Ensure that farmers use phage therapy effectively and responsibly to maximize benefits without causing adverse effects to the environment or their crops.
  • Design: Farmers should receive training on how to apply phages correctly. Governments and biotech companies can provide educational tools and resources.
  • Assumptions: It is assumed that farmers will be willing to adopt new technologies, though there may be barriers in terms of access to training and confidence in phage security.
  • Risks of Failure & “Success”: If farmers do not apply the therapy correctly, they may waste resources. There could be also resistance of adoption due to lack of experience. A “success” in adopting good practices could increase productivity.

• Action 2: Participate in initiatives to monitor and track the effectiveness of phage therapy

  • Purpose: Ensure that farmers collaborate with researchers to provide data on the effectiveness of phages in the field.
  • Design: Farmers must share their observations and results with biotech companies and researchers.
  • Assumptions: It is assumed that farmers will be willing to collaborate and share information, although this may be challenging if they do not perceive a direct benefit.
  • Risks of Failure & “Success”: If farmers do not collect accurate data, inconsistencies in results will arise. A “success” could allow for continuous improvement of the therapy, but it would depend on the collaboration and commitment of farmers.

• Action 3: Promote the use of complementary agricultural technologies with phages.

  • Purpose: Encourage the use of a more systems approach to crop management that combines phage therapy with other sustainable agricultural practices, such as integrated pest management.
  • Design: Farmers should be trained on how to combine phages with other crop management strategies (e.g., using natural predators or resistant plants) for more effective pest control.
  • Assumptions: It is assumed that farmers will be open to adopting a more integrated approach to agriculture, although this may be a challenge if they are accustomed to conventional methods.
  • Risks of Failure & “Success”: Failure could occur if farmers do not properly combine technologies or if they are not given enough guidance. A “success” could lead to more sustainable farming practices, but it could be difficult if farmers do not have access to complementary technologies.

Actor 2. Academic Researchers

• Action 1: Develop specific safety and hygiene protocols for handling phages**

  • Purpose: Ensure that phage handling in the lab is performed safely, minimizing contamination or exposure risks.
  • Design: Researchers must collaborate with biosecurity authorities to establish standardized protocols. Adequate infrastructure and resources are needed to train the staff.
  • Assumptions: It is assumed that the laboratory infrastructure will be suitable for these practices and that researchers are committed to implementing the protocols rigorously.
  • Risks of Failure & “Success”: If the protocol is not implemented correctly, there could be exposure risks to unwanted pathogens. A “success” could imply too much bureaucracy, which might hinder the flexibility needed for research.

• Action 2: Collaborate on the continuous evaluation of environmental safety of phage use

  • Purpose: Continuously assess the effects of phages on the environment, ensuring that no toxic by-products or unintended ecological impacts arise.
  • Design: An environmental research team is needed to monitor the impacts of phage use in various ecosystems. Funding is necessary to conduct these studies.
  • Assumptions: It is assumed that there will be effective cooperation between biotechnological research teams and environmental protection teams.
  • Risks of Failure & “Success”: A failure might occur if environmental studies are not conducted properly, which could lead to ecological damage. A “success” could lead to environmental control, but it may be costly and limit the use of phage therapy in certain areas.

• Action 3: Publish and disseminate scientific advances to foster transparency

  • Purpose: Promote transparency about the advances and results obtained in phage therapy research, building trust within the scientific community and the public.
  • Design: Researchers must publish their results in open-access scientific journals and collaborate with international organizations to maintain disclosure standards.
  • Assumptions: It is assumed that the scientific community is willing to share data openly and transparently.
  • Risks of Failure & “Success”: If results are not shared properly, public trust could be lost. A “success” in dissemination could lead to excess expectations and demands from the community, which might not be sustainable.

Actor 3. Government Regulators

• Action 1: Establish clear regulations for the authorization and use of phage therapies

  • Purpose: Create a regulatory framework to ensure the safety and effectiveness of phage therapy before its commercialization.
  • Design: A regulatory commission must be created to work with biotechnology, biosecurity, and public health experts to define the regulations. Stakeholders must fund continuous monitoring of these products.
  • Assumptions: It is assumed that the regulatory framework will be flexible enough to adapt to the evolution of the technology.
  • Risks of Failure & “Success”: A lack of clarity in the regulations could delay the introduction of effective therapies. A “success” could lead to regulatory overload, which might slow down innovation.

• Action 2: Promote incentives for public and private phage therapy research

  • Purpose: Provide fiscal incentives and funding to promote research in phage therapy that adheres to safety and bioethical standards.
  • Design: The government should create grant programs and tax exemptions. Public and private institutions must collaborate in research, with an audit system to ensure compliance with regulations.
  • Assumptions: It is assumed that research institutions will accept these incentives, and sufficient funds will be allocated for sustainable research.
  • Risks of Failure & “Success”: Failure could result in misuse of incentives for low-quality research. A “success” could accelerate progress, but quality control might decrease.

• Action 3: Implement supply chain traceability through blockchain technology

  • Purpose: Ensure that all phage-based products are traceable from development to their application in agriculture or medicine.
  • Design: The government must approve and implement a blockchain-based digital infrastructure, and companies must adapt to this system to ensure transparency.
  • Assumptions: It is assumed that companies will be willing to invest in blockchain technology to ensure traceability.
  • Risks of Failure & “Success”: If not properly implemented, this could result in an expensive and complicated system to manage. A “success” would improve consumer trust, but could be difficult to implement in all regions.

Actor 4. Biotech Companies

• Action 1: Develop phage-based biocontrol products following fair trade standards

  • Purpose: Create phage-based biocontrol products that respect fair trade standards, ensuring ethical and accessible distribution.
  • Design: Companies must work with fair trade certifiers to ensure that products are produced and distributed in line with these norms.
  • Assumptions: It is assumed that companies will be willing to invest in complying with these standards, although smaller producers may face challenges.
  • Risks of Failure & “Success”: A failure could occur if fair trade certification is not obtained or if accessing fair trade markets is difficult. A “success” could make production more expensive, but it would have a positive impact on equity.

• Action 2: Implement rigorous quality and safety controls for products

  • Purpose: Ensure that phage-based biotechnology products are safe, effective, and stable.
  • Design: Companies must create quality control units within their manufacturing processes and perform continuous safety testing.
  • Assumptions: It is assumed that companies have the resources and staff necessary to implement rigorous controls.
  • Risks of Failure & “Success”: A failure could result in inadequate quality control, putting consumers at risk. A “success” could increase operational costs, but would guarantee safe and effective products.

• Action 3: Promote education and awareness about the benefits and risks of phages

  • Purpose: Increase public understanding of the benefits and limitations of phage therapy, creating an informed consumer base.
  • Design: Companies must develop educational materials and interact with agricultural and medical communities to inform them about the responsible use of phages.
  • Assumptions: It is assumed that communities will be open to learning about this emerging technology.
  • Risks of Failure & “Success”: Failure could result in a lack of interest or understanding from the target audience. A “success” could change mindsets, but confusion may arise if risks are not clearly communicated.

4. Scoring Scale and Evaluation

For the evaluation of the policies, actors and actions, I propose the following scoring scale:

• A. Excellent: Strongly meets the objective.
• B. Good: Meets the objective but with some limitations.
• C. Fair: Partially meets the objective, requires improvement.
• D Poor: Does not effectively meet the objective.
• N/A. Not Applicable: The action does not impact this category.

Finally, we obtain the following table:

Week 2 HW: DNA Read, Write and Edit

Lecture Preparation

Questions from Professor Jacobson

• 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?
  • Polymerase has an error rate that ranges from about 1 in 10,000 to 1 in a million. While this may seem like a lot, the human genome is made up of approximately 3 billion base pairs, meaning that errors in replication could accumulate quickly. But biology has its own solution: it uses various proofreading mechanisms built into the polymerase, as well as repair systems like the MutS complex, which catch and correct mistakes during the replication process, ensuring that the genome stays accurate over time despite the occasional slip-up.
• 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?
  • When we talk about how many different ways we can code for an average human protein, there are multiple codons that can encode the same amino acid, thanks to the redundancy in the genetic code. This means that the system has a bit of flexibility in how proteins are made. But not all these possible codons are equally efficient. Some codons are preferred over others. It’s like a game of chess, where there are many possible moves, but certain ones are more likely to lead to victory. In this case, a properly folded and functional protein.

Questions from Dr LeProust

• What’s the most commonly used method for oligo synthesis currently?
  • I believe that the most commonly used method is phosphoramidite chemistry. A method based in the coupling of nucleotides to a growing chain of DNA, followed by oxidation, capping unreacted sites, and deblocking, with each step repeated in cycles
• Why is it difficult to make oligos longer than 200nt via direct synthesis?
  • Is difficult due to issues of error accumulation and yield loss.
• Why can’t you make a 2000bp gene via direct oligo synthesis?
  • For long sequences such that, the error rate is too high, leading to incomplete or incorrect sequences. Also, the cost and time required is really high, so it is not suitable for such synthesis.

Questions from George Church

• 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 are Arginine (Arg), Histidine (His), Methionine (Met), Isoleucine (Ile), Leucine (Leu), Lysine (Lys), Phenylalanine (Phe), Threonine (Thr), Tryptophan (Trp), and Valine (Val). Their are called essential because animals cannot synthesize and we have to obtain them in the diet. The Lysine Contingency, introduced in Jurassic Park, makes no sanse from that point of view. This is a genetic mechanism that is supposed to make dinasours dependent to substances including lysine. However in real life, any animal is capable to produce lysine. Herbivores obtain lysine from plants, and carnivores obtain lysine by eating other herbivores. In the movie, dinasours are capable of eating other animals, or humans, so the lysine contingency would apply.
• What code would you suggest for AA:AA interactions?
  • I would propose a simple sistem using the three letters name of the AA, the simbol (-) to represent the bond and the name of the other AA, e.g Lau-Lys. Another sistem would be mapping each of the 20 AA to single-letter codes (A-Z). This sistem also allows to subdive other charactarestics of the AA such as Nonpolar/Hydrophobic, Polar/Uncharged, Acidic/Basic behavior.
• Given the one paragraph abstracts for these real 2026 grant programs sketch a response to one of them or devise one of your own:
  • BioStabilization Systems recovered from https://arpa-h.gov/explore-funding/programs/boss. I am particularly interested in stabilization. In my thesis project I delved into the topic of nanoparticle stabilization in polymer matrices. Following that, I had the opportunity to participate in the mini-symposium “Bacteriophages in Science and in Practice,” organized by the Institute of Biochemistry and Biophysics PAS. One of the talks addressed the stabilization of phages in natural extracts such as essential oils and in polymers like gelatin. I really liked this approach because I believe that the solution to stabilizing chemical systems (nanoparticles stabilized in a colloidal polymer solution) or biological systems (phages in a buffer with a polymer or extract) is closely linked to materials science. Personally, I’m interested in green synthesis and natural extracts, so I would propose a stabilization method using ideas from these areas. I would propose an experiment with different buffers: one with SM Buffer, another with SM + Natural Extract, and another with SM + Natural Extract + Biocompatible Polymer, and evaluate phage production in each.

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project