Week 1 HW: Principles and Practices

Tool Description

Biosensor for the detection of stress or diseases in plants useing Escherichia coli chassis.

In this system, stress signals or specific markers associated with certain pathogens induce the production of a fluorescent protein like GFP. This biosensor could be used as a tool for the early detection of plant pathologies by exposing the bacteria to the plant extracts or exudates. T

he system could be build: a. to respond to a group of markers related to plant infection or to a group of markers for a certain pathogen. b. to detect if the plant is under abiotic stress or is infected, resulting in the production of different signals depending on the diaggnose.

Plants under abiotic stress and plants affected by pathogens often show similar external symptoms, but at a molecular level these two conditions can be differentiated. A biosensor capable of responding differentially to this conditions or only to one of these conditions could help distinguish between them, enabling more appropiate interventions

Governance Goals

1. Ambiental Security: we must avoid ambiental damage

   • Use a non pathogen strain as a chasis
   • the biosensor must be manipulated in a laboratory
   • propeer disposal of the material that has been in contact with the biosensor
   • Proper use of the tool

2. Inclusion

• disminish costs
• make the tool accesible for small productors

3. Responsible interpretation and use of results: missinterpretation of the output could lead to incorrect interventions

• Ensure that the biosentor results are presented as screening tools
• Provide clear guidance on the limitantions of the biosinsor´s accuracy

Governance Actions

1. Stablish requirements of use

• Purpose:The biosensor is based on a genetically modified organism. This action proposes establishing its use exclusively in laboratories with the required biosafety level in order to avoid the accidental spread of the organism into the ecosystem.
• Design: For this to work, a group of professionals must create a guide for use and establish requirements for purchasing the product. Users of the product must follow the provided guidelines and instructions.
• Assumptions: It is assumed that trained personnel will follow the guide for use and will not misuse the product.
• Risks of Failure & “Success”: Unresponsible personnel may misuse the biosensor, leading to the accidental release of the bacteria into the environment.

2. Propper disposal of the material

• Purpose: Ensure that users have the appropriate means for the proper disposal of materials, and monitor correct disposal in order to prevent environmental contamination.
• Design: Institutions and laboratories using the iosensor must provide approved disposal systems for biological waste, such as sterilization or inactivation procedures. Clear disposal protocols must be included in the user guide, and compliance should be overseen by institutional biosafety committees.
• Assumptions: It is assumed that that users will follow established disposal protocols.
• Risks of Failure & “Success”: disposal procedures may not be properly followed or enforced, leading to unintended release of genetically modified bacteria.

3. Result interpretation guidelines
   • Purpose:Prevent misinterpretation of biosensor outputs by ensuring that results are understood as indicative signals rather than definitive diagnoses.
   • Design:Develop standardized interpretation guidelines that accompany the biosensor, including clear explanations of what a positive or negative signal means and its limitations. These guidelines should be created by academic experts and included in the user manual.
   • Assumptions: It is assumed that users follow the interpretation guidelines when analyzing results.
   • Risks of Failure & “Success”: users may ignore or oversimplify the guidelines.

Priorization of gocernance options

Based on the scoring, the governance options that should be prioritized are establishing requirements of use and result interpretation guidelines, while proper disposal of materials functions as a complementary measure.

Requirements of use are essential because they directly reduce risks related to biosecurity, laboratory safety, and environmental protection by limiting the biosensor to controlled laboratory settings. However, these requirements may increase costs and restrict access, particularly for smaller laboratories.

Result interpretation guidelines are a high-priority complementary action because they are easy to implement, low cost, and help prevent incorrect decisions based on biosensor outputs. Since the biosensor is intended as a screening tool, clear guidance is necessary to avoid inappropriate interventions.

Proper disposal of materials is also important but relies strongly on infrastructure and enforcement, which can vary between institutions.

Homework Questions from Professor Jacobson:

1. Nature’s machinery for copying DNA is called polymerase.
   • What is the error rate of polymerase? 1/10⁶
   • How does this compare to the length of the human genome? The human genome is approximately 3 × 10⁹ base pairs long. At this error rate, thousands of errors would be expected per replication cycle if no correction mechanisms were present
   • How does biology deal with that discrepancy?1. polymerases can detect and corect errors (proofreading activity); 2. Cells have repear sytems to correct DNA mutations (like MutS system)
2. How many different ways are there to code (DNA nucleotide code) for an average human protein? There are many ways to code for an average human protein due to the degeneracy of the genetic code: each aminocid is encoded by two or three codons. In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest? The use of codons differs between organisms; that is, some organisms commonly use codons that are rare in others. As a consequence, the translation efficiency of a human protein expressed in yeast or bacteria can be limited due to the low availability of the corresponding tRNAs. Another reason is the absence or differences in post-transcriptional and post-translational modifications between expression systems (such as bacteria or yeast) and human cells, which can affect protein folding, stability, and functionality.

Homework Questions from Dr. LeProust:

What’s the most commonly used method for oligo synthesis currently? Solid-phase chemical synthesis, specifically phosphoramidite chemistry, is the most widely used method for oligonucleotide synthesis. Why is it difficult to make oligos longer than 200nt via direct synthesis? Because error in nucleotid addition accumulates with increasing length, leading to a sharp drop in yield and sequence fidelity for longer oligonucleotides. Why can’t you make a 2000bp gene via direct oligo synthesis? Considerieng the avobe, direct syhthesis of a 2000bp gene would result in an unacceptably high error rate and extremely low yield.

Homework Question from George Church:

[Using Google & Prof. Church’s slide #4]

• What are the 10 essential amino acids in all animals? **H, I, L K, M, F(Phe), T, W, V and R.
• How does this affect your view of the “Lysine Contingency”? The “Lysine Contigency” could have made scence if the dinosaurs had have been genetically engineered to be able to produce all essential amino acids except lysine, so that they would survive only with lysine supplementation (and not the rest of the essential amino acids), and die when supplementation was withdrawn.

IA prompts: Q: Which are the 10 essential aa in animals? A:The 10 essential amino acids in animals are:

1. Histidine
2. Isoleucine
3. Leucine
4. Lysine
5. Methionine
6. Phenylalanine
7. Threonine
8. Tryptophan
9. Valine
10. Arginine