Week 1 HW: Principles and Practices

Homework 1 - Due February 10th

1. First, describe a biological engineering application or tool you want to develop and why.** This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about.

Coral reefs are one of the most biodiverse ecosystems on Earth, but they are increasingly threated due to climate change, and pollution that cause widespread coral bleaching. Bleaching happens when the temperature stress disrupts the symbiotic relationship between corals and their photosynthetic symbionts, leading to increased ROS production, tissue damage, and starvation.

In this homework assignment, I’ll be exploring the possibility of bioengineering coral symbionts (like the algae, Symbiodiniaceae) or other associated microbes to improve tolerance to the temperature changes and oxidative stress.

By strenghtening these symbionts, we aim to reduce coral mortality during extreme heat, while also helping existing conservation efforts in maintaining them and the habitat they provide.

Ethical, environmental and governance challenges come into play when introducing an engineered organism into an already fragile marine ecosystem, making this a good topic for this assignment.

2. Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals.

First Goal: Prevent ecological harm

• Prevent irreversible ecosystem disruption

Second Goal: Ensure environmental safety

• Early detection and responses to issues
• Responsibilities assigned clearly

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”).

1 - Regulatory, contained field trials Purpose: Reef interventions are usually small scale or unregulated, so we introduce a mandatory phased trial after the lab and limit reef deployment in case something happens Design: National environment regulators implement it, risk assessments are done before the phase trials even start, and mandatory criteria to hit to continue on Assumptions: Small scaled trials will accurately predict ecosystem wide effects Risks of failue and success: Failure = containment fails and organisms spread when they aren’t supposed to Success = slow introduction could delay help to rapidly declining reefs

2 - Techninal, genetic and ecological safeguards Purpose: reduce risks associated with persistence and spread of engineered symbionts Design: self-limiting genes, stress induced slowing, developed by researchers and verified by regulators Assumptions: minimal or no horizontal gene transfer Risks of failure and success: Failure = mutations will disable safeguards Success = more oversight if rely too much on safeguard

3 - Policy, International reef governance Purpose: Coral reefs can cross national boundaries, so international coordination for reef bioengineering interventions Design: coordinated by international bodies like the UN or marine organizations, shared standards for trials, monitoring and public reports, and also inclusion of indigenous communities in the varying nations Assumptions: Nations are willing to work together or give up some autonomy, and adhere to new global standards, and comply and trust each other Risks of failure or success: Failure = nations being stubborn lead to delays in urgent action Success = a one size fits all standard may ignore ecological differences based on geographical needs and location.

4. Next, score (from 1-3 with, 1 as the best, or n/a) each of your governance actions against your rubric of policy goals. The following is one framework but feel free to make your own:

1 = best, 3 = worst

5. Last, drawing upon this scoring, describe which governance option, or combination of options, you would prioritize, and why. Outline any trade-offs you considered as well as assumptions and uncertainties.

Based on the scoring in the table in question 4, the most reasonable approach would be a combination of options 1 and 2, but we could also use some elements from option 3.

• Phased trials ensure accountability and caution
• Genetic safeguards reduce risks
• International coordination are valuable but localized action might be better for faster response

Trade-offs to consider:

• Speed compared to safety in climate emergency
• Global standards compared to local ecological knowledge
• Innovation in science compared to irreversible environmental risk

Target audience: I would aim my recommendation at national environmental regulators, international marine governance bodies, and research institutions that are conducting reef research / reef interventions.

Reflection Not that it was specifically mentioned in the lecture, but while listenting to examples and being able to make drawbacks to my own ideas, some ethical concerns that came up for me for my project are the environmental risks. As in this could do more harm than good, or not enough good to be worth it. It could be irreversible and once the engineered organisms are released it’ll be hard to remove them if need be. Also, the issue in morality comes in when I think of; who has the right to alter an ecosystem if the benefits cannot be guaranteed?

Additional governance actions to address these concerns could be mandatory public engagement and stricter consequences. People who destroy reefs will be ounished more severely, but the public will also be more involved in it’s conservation.

Week 2 HW

Part 1: Benchling & Gel Art

Benchling Lambda DNA Gel with various enzymes

Benchling Lambda DNA Linear Map with various enzymes

Benchling Lambda DNA Art!!! XXXX put art screenshot here XXXX

Part 2: In person lab - N/A

Part 3: DNA design challenge

3.1. Choose your protein. I chose myoglobin

• Myoglobin is a protein that transports oxygen around skeletal and cardiac muscles, and scavenges nitric oxide.
• I found myoglobin interesting because of it’s prevalence in mammals that dive in water, like whales and dolphins, where in there muscles, higher concentrations of myoglobin can be found.

NCBI protein sequence for myoglobin (specifically: myoglobin isoform 1 [Homo sapiens])

• NCBI Reference Sequence: NP_001369738.1
• MGLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASEDLKKHGATVLTALGGILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISECIIQVLQSKHPGDFGADAQGAMNKALELFRKDMASNYKELGFQG

ex from HGTAA:

sp|P03609|LYS_BPMS2 Lysis protein OS=Escherichia phage MS2 OX=12022 PE=2 SV=1 METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLL EAVIRTVTTLQQLLT

3.2. Reverse Translate: Protein (amino acid) sequence to DNA (nucleotide) sequence.

The Central Dogma discussed in class and recitation describes the process in which DNA sequence becomes transcribed and translated into protein. The Central Dogma gives us the framework to work backwards from a given protein sequence and infer the DNA sequence that the protein is derived from. Using one of the tools discussed in class, NCBI or online tools (google “reverse translation tools”), determine the nucleotide sequence that corresponds to the protein sequence you chose above.

Reverse translation result using bioinformatics.com

• reverse translation -> most likely codons atgggcctgagcgatggcgaatggcagctggtgctgaacgtgtggggcaaagtggaagcggatattccgggccatggccaggaagtgctgattcgcctgtttaaaggccatccggaaaccctggaaaaatttgataaatttaaacatctgaaaagcgaagatgaaatgaaagcgagcgaagatctgaaaaaacatggcgcgaccgtgctgaccgcgctgggcggcattctgaaaaaaaaaggccatcatgaagcggaaattaaaccgctggcgcagagccatgcgaccaaacataaaattccggtgaaatatctggaatttattagcgaatgcattattcaggtgctgcagagcaaacatccgggcgattttggcgcggatgcgcagggcgcgatgaacaaagcgctggaactgtttcgcaaagatatggcgagcaactataaagaactgggctttcagggc

reverse translation -> consensus codons atgggnytnwsngayggngartggcarytngtnytnaaygtntggggnaargtngargcngayathccnggncayggncargargtnytnathmgnytnttyaarggncayccngaracnytngaraarttygayaarttyaarcayytnaarwsngargaygaratgaargcnwsngargayytnaaraarcayggngcnacngtnytnacngcnytnggnggnathytnaaraaraarggncaycaygargcngarathaarccnytngcncarwsncaygcnacnaarcayaarathccngtnaartayytngarttyathwsngartgyathathcargtnytncarwsnaarcayccnggngayttyggngcngaygcncarggngcnatgaayaargcnytngarytnttymgnaargayatggcnwsnaaytayaargarytnggnttycarggn

[Example: Get to the original sequence of phage MS2 L-protein from its genome phage MS2 genome - Nucleotide - NCBI]