Week 1 HW: Principles and Practices

HOMEWORK 1

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.

One of the main reasons I am interested in synthetic biology is because I see it as a real and accessible bridge between design and biology, as well as a key pathway toward the future of design applied to living systems. Throughout my experience as a designer, I have developed a growing interest in reducing the gap between what is created by humans and natural systems. Often, even when design draws inspiration from nature, it remains an exclusively human interpretation. This has led me to question what the true role of the designer should be when working with living systems and natural environments. In this context, I am deeply interested in the future exploration of synthetic morphogenesis, understood as the possibility of creating biological frameworks that allow materials or living systems to develop their own form and function autonomously through natural processes. From this perspective, the designer does not necessarily define the final outcome but rather facilitates the initial conditions that allow nature to actively participate in the creative process. I believe synthetic biology can offer tools to advance toward these kinds of practices, where our role is to design conditions rather than impose forms. However, while recognizing that this concept still requires deeper development, specific areas already exist where certain approaches and principles can begin to be explored and consolidated. As a design professional, I have always felt a strong call to action to create solutions that not only improve people’s quality of life but also contribute to a broader ecosystemic perspective on wellbeing. My interest is not limited to human benefit; rather, I aim to explore how design can help care for, regenerate, and strengthen the natural environments and living systems upon which we depend. This vision has led me to explore fields such as bio-inspired design, biomimetics, bionics, and ultimately biodesign. Throughout this trajectory, one of my main interests has been design oriented toward conservation and ecological remediation, particularly within marine ecosystems. My recent work has focused on exploring design- and material-based solutions that contribute to the regeneration of marine environments affected by climate change. In recent years, I have become particularly interested in developing proposals to mitigate the impact of ocean acidification. Ocean acidification is a global issue caused by increasing atmospheric CO₂ levels, which alter seawater chemistry and reduce pH levels. This phenomenon decreases the availability of calcium carbonate (CaCO₃), an essential component for calcifying organisms such as corals, mollusks, and crustaceans, affecting their ability to form skeletal structures through biomineralization and reducing their chances of survival. Many of these organisms play a fundamental role at the base of marine food webs and in the functional structure of ecosystems; therefore, significant alterations in their populations can trigger cascading effects, leading to systemic ecosystem losses and a progressive decline in biodiversity. To address this problem, various strategies have been developed worldwide, including artificial reefs and aquaculture systems. However, despite their progress, most approaches have focused primarily on structural design, leaving the biological potential of materiality relatively underexplored. For this reason, I would like to take this exploration to the next level. One of the biological engineering applications I would like to develop during the course How to Grow Almost Everything is a bioengineered living material that initially functions as a bioreceptor for CaCO₃ particles present in the water, attracting and concentrating them to facilitate the formation of artificial reefs in strategic locations. In alignment with my interest in synthetic morphogenesis, I would also like to explore the possibility that this material not only performs a capture function but is capable of growing, self-organizing, and adopting its own configurations through biological processes, contributing to the formation of structures that emerge from natural dynamics rather than from fully predetermined human designs. Through this approach, it would be possible to locally increase the availability of calcium carbonate, support biomineralization processes, and contribute to restoring ecological balance in areas affected by ocean acidification, generating benefits for both marine ecosystems and the human communities that depend on them.

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. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy.

(1) Promote ecological restoration and Long-Term ecosystem balance -Ensure the material supports native calcifying organisms and does not displace or outcompete existing species. -Require ecological impact assessments prior to deployment in new marine environments. -Prioritize deployment in degraded or climate-vulnerable areas where restoration potential is scientifically justified.

(2) Enhance ecosystem services while preserving biodiversity integrity -Design materials to support habitat formation, biodiversity recovery, and coastal protection without creating monocultures. -Monitor long-term ecological outcomes such as species diversity, trophic balance, and reef resilience.

(3) Strengthen Socio-Ecological resilience by enhancing ecosystem services -Facilitate the recovery of marine food webs that sustain fisheries and coastal economies. -Improve ecosystem services such as habitat formation, biodiversity support, and climate adaptation. -Promote long-term ecological stability as the foundation for human wellbeing.

(4) Promote responsible and collaborative marine stewardship Facilitate coordinated decision-making between research institutions, environmental agencies, and coastal communities involved in marine restoration efforts. Encourage transparent monitoring, shared scientific data, and collective ecological oversight across regions. Support equitable access to knowledge and responsible deployment practices that prioritize long-term ecosystem health and social wellbeing.

3. Next, describe at least three different potential governance “actions” by considering the four aspects below (Purpose, Design, Assumptions, Risks of Failure & “Success”). Try to outline a mix of actions (e.g. a new requirement/rule, incentive, or technical strategy) pursued by different “actors” (e.g. academic researchers, companies, federal regulators, law enforcement, etc). Draw upon your existing knowledge and a little additional digging, and feel free to use analogies to other domains (e.g. 3D printing, drones, financial systems, etc.).
   • Purpose: What is done now and what changes are you proposing?
   • Design: What is needed to make it “work”? (including the actor(s) involved - who must opt-in, fund, approve, or implement, etc)
   • Assumptions: What could you have wrong (incorrect assumptions, uncertainties)?
   • Risks of Failure & “Success”: How might this fail, including any unintended consequences of the “success” of your proposed actions?

1.Controlled Access and Authorized Deployment Framework

While projects focused on the implementation of artificial reefs largely aim to benefit marine ecosystems, their direct interaction with complex natural environments means that inadequate planning or mismanagement could produce outcomes contrary to those intended. This concern becomes even more significant when considering the deployment of a bioengineered living material with active interaction within marine ecosystems. For this reason, the first proposed governance action is the establishment of a controlled access and regulated deployment framework, in which the use and implementation of this material would be authorized exclusively for public research institutions operating in formal collaboration and joint monitoring with governmental environmental agencies and organizations specialized in ecological restoration. Such a model would help reduce the risk of irresponsible or insufficiently supervised applications while promoting evidence-based interventions grounded in long-term ecosystem planning. Additionally, each deployment should be subject to prior ecological impact assessments and continuous monitoring systems capable of adapting interventions according to ecosystem responses over time. Nevertheless, this approach may also face challenges, including administrative processes that could slow urgent restoration efforts or institutional limitations in sustaining long-term oversight.

2.Creation of an International Marine Bioengineering Association

Oceans are not uniform and present unique ecological, chemical, and biological characteristics depending on the regions in which they are located; however, any intervention in these systems may generate transboundary ecological effects. In this context, most marine restoration initiatives continue to be managed primarily at local or national levels, which may limit a comprehensive understanding of their impacts and reduce their effectiveness at broader scales. Therefore, the creation of an international marine bioengineering governance association is proposed to coordinate shared standards, biosafety protocols, and collaborative ecological assessment frameworks across countries. As part of this initiative, it would be essential to establish an international network of authorized laboratories and research centers with regulated access to these types of materials, facilitating collaborative monitoring of their use, the exchange of scientific data, and the planning of interventions at regional and global scales. This approach would strengthen local actions through a broader ecosystem-based perspective, promoting informed decision-making and adaptive strategies grounded in shared scientific evidence. Nevertheless, this model may also face important challenges, including difficulties in political coordination between countries and inequalities in access to the scientific and technological resources necessary for its effective implementation.

3.Biosecurity & Environmentally Controlled Activation of Living Material

Beyond regulatory and institutional frameworks, a third governance action involves integrating principles of ecological responsibility directly into the functional design of the living material from its earliest stages of development. Considering that the material’s primary objective is to act as a bioreceptor capable of attracting and concentrating calcium carbonate (CaCO₃) particles present in the water to facilitate natural biomineralization processes in nearby marine organisms, it is essential to establish clear limits on its ecological behavior and its interaction with the surrounding environment. In this regard, the material could be designed to remain functionally inert under normal environmental conditions and to activate only under specific scenarios of marine acidification, responding to defined physicochemical parameters associated with ecosystem imbalance. This conditional activation would help reduce the risk of unintended alterations to local ecological dynamics, promoting a strategy of “responsibility by design” in which researchers, biological designers, and academic institutions integrate ethical and ecosystem-based considerations from the outset of technological development.

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:

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. For this, you can choose one or more relevant audiences for your recommendation, which could range from the very local (e.g. to MIT leadership or Cambridge Mayoral Office) to the national (e.g. to President Biden or the head of a Federal Agency) to the international (e.g. to the United Nations Office of the Secretary-General, or the leadership of a multinational firm or industry consortia). These could also be one of the “actor” groups in your matrix.

From my personal perspective, the key element of this project lies in the strategic development of materials specifically designed to minimize the impacts of ocean acidification. Building on this foundation, a comprehensive strategic plan should be developed in collaboration with governmental entities to ensure a conscious, well-structured approach directed exclusively toward ecological restoration. Such coordination would allow for responsible implementation, clear environmental oversight, and long-term sustainability aligned with conservation priorities.

Week 2 HW

Class Assignment Homework 2

Part1: Benchling & In-sico GelArt See this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis” for details. Overview: Make a free account at benchling.com Import the Lambda DNA. Simulate Restriction Enzyme Digestion with the following Enzymes: EcoRI HindIII BamHI KpnI EcoRV SacI SalI Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs!

This was my first time working with Benchling, as well as my first experience exploring the possibilities of DNA design. As a first step, I imported the Lambda DNA sequences to begin experimenting with the digestion using enzymes such as EcoRI, EcoRV, SalI, SacI, KpnI, among others. This process led me to explore combinations and fusions between these enzymes, resulting in a wide variety of sequence ladder patterns. From that point, I began manipulating the patterns by rearranging the order of the tabs, which allowed me to design and create my own custom sequence design.

Now behold the first robot, made with 100% dna Enzymes.

3.1. Choose your protein.

In recitation, we discussed that you will pick a protein for your homework that you find interesting. Which protein have you chosen and why? Using one of the tools described in recitation (NCBI, UniProt, google), obtain the protein sequence for the protein you chose. [Example from our group homework, you may notice the particular format~~~ The example below came from UniProt] sp|P03609|LYS_BPMS2 Lysis protein OS=Escherichia phage MS2 OX=12022 PE=2 SV=1 METRFPQQSQQTPASTNRRRPFKHEDYPCRRQQRSSTLYVLIFLAIFLSKFTNQLLLSLL EAVIRTVTTLQQLLT

For the second week of the HTGAA course, I chose a molluscan shell matrix protein involved in calcium carbonate biomineralization, called mantle protein N25 (N25). This protein is found in the calcifying organism Pinctada fucata, commonly known as the Akoya pearl oyster. N25 is part of the shell matrix and helps regulate calcium carbonate biomineralization, playing a key role in crystal growth, morphology, and the formation of microscopic calcifying structures. I want to explore this protein because my goal is to engineer a material for artificial reefs that can act as a “magnet” for dissolved calcium carbonate in seawater, creating localized microenvironments that favor CaCO₃ deposition and make carbonate more accessible for calcifying organisms affected by ocean acidification.

IMAGE FROM:https://www.newscientist.com/article/2151281-oysters-can-hear-the-ocean-even-though-they-dont-have-ears/

Yang, D., Yan, Y., Yang, X., Liu, J., Zheng, G., Xie, L., & Zhang, R. (2019). A basic protein, N25, from a mollusk modifies calcium carbonate morphology and shell biomineralization. Journal of Biological Chemistry, 294(21), 8371–8384. https://doi.org/10.1074/jbc.RA118.007338

Using UniProt, I obtained the amino acid sequence of mantle protein N25 (N25):

**FASTA

tr|A0A0E3XA28|A0A0E3XA28_PINFU Mantle protein N25 OS=Pinctada fucata OX=50426 PE=2 SV=1 MKRIYVLVLLFILLVCIAEAQKKSKDSKKASSKSSSKSSGKSKSSPKSSGAKGKSPAPSA PASKGPSEMQKLAEEMVALSNRLLKAIKAGEQMPPPMCPNGLPKADCSPLACDKWTCSNI LNTVCKEQCHVCEPKFYIGGSEVTQFCELKPANMQPRATQSPPTSRNTATDQGPQNSGPS SNGAPSNMPPMPGMPMMFSENPMPMGGPPGMEFMPNFENFPPGMSPMQFFHHLQNMNMPN ENQGSRSQAN**

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

To reverse translate the mantle protein N25 amino acid sequence to DNA, I used the online reverse translation tool at novoprolabs.com/tools/revtrans.

N25 protein DNA sequence atgaaacgcatttatgtgctggtgctgctgtttattctgctggtgtgcattgcggaagcgcagaaaaaaagcaaagatagcaaaaaagcgagcagcaaaagcagcagcaaaagcagcggcaaaagcaaaagcagcccgaaaagcagcggcgcgaaaggcaaaagcccggcgccgagcgccggcgagcaaaggcccgagcgaaatgcagaaactggcggaagaaatggtggcgctgagcaaccgcctgctgaaagcgattaaagcgggcgaacagatgccgccgccgatgtgcccgaacggcctgccgaaagcggattgcagcccgctggcgtgcgataaatggacctgcagcaacattctgaacaccgtgtgcaaagaacagtgccatgtgtgcgaaccgaaattttatattggcggcagcgaagtgacccagttttgcgaactgaaaccggcgaacatgcagccgcgcgcgacccagagcccgccgaccagccgcaacaccgcgaccgatcagggcccgcagaacagcggcccgagcagcaacggcgcgccgagcaacatgccgccgatgccgggcatgccgatgatgtttagcgaaaacccgatgccgatgggcggcccgccgggcatggaatttatgccgaactttgaaaactttccgccgggcatgagcccgatgcagttttttcatcatctgcagaacatgaacatgccgaacgaaaaccagggcagccgcagccaggcgaac

3.3 Codon optimization.Once nucleotide sequence of your protein is determined, you need to codon optimize your sequence. You may, once again, utilize google for a “codon optimization tool”. In your own words, describe why do you need to optimize codon usage. Which organism have you chose to optimize the codon sequence for and why?

I recently discovered what codons are and the key role they have in the protein formation process. They function as coordinates to encode amino acids. In the world, there are 64 possible codons for the 20 types of amino acids, which means that different codons can encode the same amino acid. That being said, codon optimization is necessary because different organisms prefer some codons over others due to DNA reading bias. This is a vital step to create a more effective way to reproduce genes from one organism to another. Although the genetic code is universal, certain organisms preferentially use specific codons due to differences in tRNA abundance and translation efficiency.

For this project, I optimized the codon sequence for expression in Bacillus subtilis. I selected Bacillus subtilis because:

It is genetically well-characterized It is widely used in biotechnology It can secrete proteins extracellularly It tolerates moderate saline environments

This process was performed using an online codon optimization tool. The optimized sequence maintains the same amino acid sequence but improves translational efficiency in the chosen host organism.

3.4 You Have a sequence! Now What? With the codon-optimized DNA sequence of N25, the protein can be produced using a cell-dependent system with Bacillus subtilis as the host. The optimized DNA is introduced into the bacteria through transformation. Inside the cells, the DNA is transcribed into mRNA and then translated by ribosomes into the N25 protein.

Bacillus subtilis can secrete the protein extracellularly, which simplifies collection and use. This approach leverages the host’s natural cellular machinery while ensuring that the codon optimization maximizes translation efficiency. By producing N25 in Bacillus subtilis, it is possible to generate sufficient protein for bioengineering applications, such as creating microenvironments that attract calcium carbonate for artificial reef materials.

**Part 4: Prepare a Twist DNA Synthesis Order ** This is a practice exercise, not necessarily your real Twist order! 4.1. Create a Twist account and a Benchling account

UFQ89828.1 mCherry [synthetic construct] MVSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSPQF MYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPV MQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHN EDYTIVEQYERAEGRHSTGGMDELYK

reverse translation of UFQ89828.1 mCherry [synthetic construct] to a 708 base sequence of most likely codons. atggtgagcaaaggcgaagaagataacatggcgattattaaagaatttatgcgctttaaa gtgcatatggaaggcagcgtgaacggccatgaatttgaaattgaaggcgaaggcgaaggc cgcccgtatgaaggcacccagaccgcgaaactgaaagtgaccaaaggcggcccgctgccg tttgcgtgggatattctgagcccgcagtttatgtatggcagcaaagcgtatgtgaaacat ccggcggatattccggattatctgaaactgagctttccggaaggctttaaatgggaacgc gtgatgaactttgaagatggcggcgtggtgaccgtgacccaggatagcagcctgcaggat ggcgaatttatttataaagtgaaactgcgcggcaccaactttccgagcgatggcccggtg atgcagaaaaaaaccatgggctgggaagcgagcagcgaacgcatgtatccggaagatggc gcgctgaaaggcgaaattaaacagcgcctgaaactgaaagatggcggccattatgatgcg gaagtgaaaaccacctataaagcgaaaaaaccggtgcagctgccgggcgcgtataacgtg aacattaaactggatattaccagccataacgaagattataccattgtggaacagtatgaa cgcgcggaaggccgccatagcaccggcggcatggatgaactgtataaa

4.1 (i) What DNA would you want to sequence and why?

As an industrial designer, I’m always looking for ways to improve urban lifestyles through innovative materials. With CO₂ emissions rising in cities, I would sequence DNA from engineered E. coli bacteria embedded in “bio-bricks” designed for future buildings and urban infrastructure. These bacteria act as simple CO₂ sensors: when CO₂ levels are high, they modify a specific part of their DNA to record exposure events. By sampling bacteria from different bricks across the city and sequencing this “memory region,” I could map pollution patterns over time and create bio-integrated technologies that literally store environmental data within our built environment.​

IMAGE FROM: https://www.front-materials.com/news/biomason-front-biobasedtile/

4.1 (ii) What technology would you use to perform sequencing and why?

Is your method first-, second- or third-generation or other? How so? For this project I would choose the second-generation method, specifically Illumina, since it is very accessible and efficient and allows reading millions of short DNA fragments at the same time in parallel. In contrast, first-generation (Sanger) reads one DNA molecule at a time, which is very slow, and third-generation (Nanopore, PacBio) reads complete long molecules one by one but is less precise for my case. For my bio-bricks I only need to read a specific short region of the bacterial DNA, so second generation is more accurate and pertinent.

What is your input? How do you prepare your input? List the essential steps.

As a first step in preparing the input, I would obtain samples from the bacteria in the bio-bricks by scraping their surface. As a next step, I understand that I would use Polymerase Chain Reaction (PCR) to obtain copies only of the specific DNA region where the “CO₂ memory” is stored. As a third step, I would add short adapter sequences to allow the fragments to enter the sequencing machine. I would also use a type of identification tag (barcode) for each bio-brick in order to distinguish the samples. Finally, I would mix the samples together so they can be sequenced simultaneously. What are the essential steps of your chosen sequencing technology, and how does it decode the bases of your DNA sample (base calling)? Since I chose the second-generation Illumina method, the process begins with attaching DNA fragments to a special plate called a flow cell. Once attached, the fragments are copied many times, forming small groups called clusters. Then, the machine adds one nucleotide at a time, and each incorporation generates a fluorescent color signal (for example, A is green, T is red, C is blue, and G is yellow). After each cycle, a camera takes an image of the entire plate, and a software program interprets the color detected in each cluster to determine which base was added. By repeating this process many times, the complete DNA sequence is reconstructed.

What is the output of your chosen sequencing technology?

The result I get from Illumina is a set of files that contain millions of small DNA fragments from the region where my bacteria store the “CO₂ memory.”Each sequence comes from a different group of DNA that was read by the machine, and thanks to the labels I added earlier, I can tell which bio-brick each fragment came from. With all this information, I can compare patterns between different bricks and analyze the history of CO₂ exposure in different parts of the city

4.2 DNA Write (i) What DNA would you want to synthesize (write) and why?

As a designer, I have always been interested in understanding why things have specific shapes. For that reason, I would like to synthesize simple genetic circuits related to morphogenesis — how living tissues or cell populations grow into particular forms. During the first class, the possibility of inoculating bacteria with DNA fragments to make them generate shapes or patterns inspired by much larger organisms was mentioned, but within an in vitro environment.

In the long term, and in a more speculative way, I would like to explore applying this principle to the creation of architectural modules — potentially shaping urban landscapes, or even designing products that are grown by nature itself, but guided by human intention.I am aware that this is not currently a mature technology, so I see it more as an exploratory and future-oriented design question rather than something that can be fully built today.

(ii) What technology would you use to perform this DNA synthesis and why? What are the essential steps of your chosen sequencing methods? From what I’ve understood, DNA synthesis is done by adding one base at a time in a controlled way. First, the last added base is protected, then a new base is incorporated, the bond is chemically stabilized, the remaining reagents are washed away, and the cycle is repeated until the full sequence is completed. I understand that it is a repetitive process that requires a lot of precision to obtain the correct sequence.

4.2 (ii) What are the limitations of your sequencing method (if any) in terms of speed, accuracy, scalability? One of the main limitations is the turnaround time of 2-4 weeks since chemical synthesis happens cycle by cycle, plus limitations on chain length up to 2000 bases and occasional errors of ~1 every 100-300 bases.

4.3 DNA Edit (i) What DNA would you want to edit and why?

I would like to edit a specific gene in the Peruvian scallop (Argopecten purpuratus) to make its shells more resistant to ocean acidification during the larval stage. Ocean acidification dissolves calcium carbonate shells of shellfish, and scallop larvae are especially vulnerable. This species is important for Peruvian aquaculture and coastal economies, so helping them survive better would support sustainable fisheries. The principle could also apply to oysters, mussels, and other shellfish facing the same threat.

(ii) What technology would you use and why? I understand that one of the most precise and accessible gene editing tools available today is CRISPR-Cas9, and also because it’s precise and has been used successfully in shellfish for targeted edits.

https://www.frontiersin.org/journals/marine-science/articles/10.3389/fmars.2022.912409/full

How does your technology of choice edit DNA? What are the essential steps?

I still find it hard to fully understand the principles of genetic modification, but I understand that CRISPR-Cas9 is a tool that allows cutting and editing DNA at a specific location. This tool uses an RNA molecule as a guide to select the sequence we want to modify, and then the Cas9 protein works like scissors to cut the DNA. Once the DNA is cut, it is possible to deactivate a gene or insert new sequences with different genetic information. What preparation do you need to do (e.g. design steps) and what is the input (e.g. DNA template, enzymes, plasmids, primers, guides, cells) for the editing? To change a gene that makes oysters vulnerable, you first need to identify which gene it is. Then, you use CRISPR-Cas9 with a guide RNA to find that specific gene and Cas9 to cut it like scissors. After the cut, the oyster cell can repair the DNA, and at that moment you can insert a new version of the gene that doesn’t cause vulnerability.

What are the limitations of your editing methods (if any) in terms of efficiency or precision?

CRISPR-Cas9 is not perfect. I understand that sometimes it could cut in the wrong places and damage healthy genes. Also, to carry out this process, it is necessary to do many tests to make sure it actually worked. In the case of oysters, the larvae are very fragile and some could die during the injection. In addition, it takes a lot of time, even months, to raise them and check the results.

Week 1 HW: Principles and Practices

Week 1 Lab: Pipetting

Individual Final Project

Group Final Project